From 0a5c2816ea3715529cdc4c68a78eab03ab291752 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 21 Mar 2022 19:02:42 +0100
Subject: gnu: Add r-cycombine.

* gnu/packages/bioconductor.scm (r-cycombine): New variable.
---
 gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55d397e5cf..ffa38fda3a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10066,6 +10066,49 @@ (define-public r-consensusclusterplus
 cluster count and membership by stability evidence in unsupervised analysis.")
     (license license:gpl2)))
 
+;; This is the latest commit and it solves a bug from the latest release.
+(define-public r-cycombine
+  (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
+    (package
+      (name "r-cycombine")
+      (version (git-version "0.2.6" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/biosurf/cyCombine")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
+      (properties `((upstream-name . "cyCombine")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biobase
+             r-cytolib
+             r-dplyr
+             r-flowcore
+             r-ggplot2
+             r-knitr
+             r-kohonen
+             r-magrittr
+             r-purrr
+             r-rcolorbrewer
+             r-readr
+             r-readxl
+             r-stringr
+             r-sva
+             r-tibble
+             r-tidyr))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/biosurf/cyCombine")
+      (synopsis "Integration of single-cell cytometry datasets")
+      (description
+       "This package provides a method for combining single-cell cytometry
+datasets, which increases the analytical flexibility and the statistical power
+of the analyses while minimizing technical noise.")
+      (license license:expat))))
+
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-- 
cgit v1.2.3


From 730ac9ab85b4a7662558d5158b1a7e02afdd65c3 Mon Sep 17 00:00:00 2001
From: Hong Li <hli@mdc-berlin.de>
Date: Tue, 29 Mar 2022 07:03:15 +0000
Subject: gnu: Add r-stager.

* gnu/packages/bioconductor.scm (r-stager): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ffa38fda3a..ce1e23f0bf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4739,6 +4739,29 @@ (define-public r-slingshot
 graph construction.")
    (license license:artistic2.0)))
 
+(define-public r-stager
+  (package
+    (name "r-stager")
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "stageR" version))
+       (sha256
+        (base32 "0vpx0v04hgkhzi0bm7ipnb9xr37n5wvnnr45lljgni8pwabfkf6y"))))
+    (properties `((upstream-name . "stageR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/stageR")
+    (synopsis "Stage-wise analysis of high throughput gene expression data")
+    (description
+     "The stageR package allows automated stage-wise analysis of
+high-throughput gene expression data.  The method is published in Genome
+Biology at
+@url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
+    (license license:gpl3)))
+
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-- 
cgit v1.2.3


From 3704a7b8978d510a8bbeae0a92ed60ece808f5ac Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 11 Apr 2022 13:27:27 +0200
Subject: gnu: Add r-tricycle.

* gnu/packages/bioconductor.scm (r-tricycle): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ce1e23f0bf..e6555c93df 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -775,6 +775,43 @@ (define-public r-ensdb-mmusculus-v79
 Ensembl.")
     (license license:artistic2.0)))
 
+(define-public r-tricycle
+  (package
+    (name "r-tricycle")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tricycle" version))
+              (sha256
+               (base32
+                "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r"))))
+    (properties `((upstream-name . "tricycle")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi
+                             r-circular
+                             r-dplyr
+                             r-genomicranges
+                             r-ggplot2
+                             r-iranges
+                             r-rcolorbrewer
+                             r-s4vectors
+                             r-scater
+                             r-scattermore
+                             r-singlecellexperiment
+                             r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hansenlab/tricycle")
+    (synopsis "Transferable representation and inference of cell cycle")
+    (description
+     "The package contains functions to infer and visualize cell cycle process
+using Single-cell RNA-Seq data.  It exploits the idea of transfer learning,
+projecting new data to the previous learned biologically interpretable space.
+The @code{tricycle} provides a pre-learned cell cycle space, which could be
+used to infer cell cycle time of human and mouse single cell samples.  In
+addition, it also offer functions to visualize cell cycle time on different
+embeddings and functions to build new reference.")
+    (license license:gpl3)))
+
 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
   (package
     (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
-- 
cgit v1.2.3


From ba5e32d9ceb5b26c36a30393b814cff4b1583c54 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 11 Apr 2022 18:00:56 +0200
Subject: gnu: r-nmf: Update to 0.24.0.

* gnu/packages/bioconductor.scm (r-nmf): Update to 0.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e6555c93df..46ac053a27 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2089,14 +2089,14 @@ (define-public r-jetset
 (define-public r-nmf
   (package
     (name "r-nmf")
-    (version "0.23.0")
+    (version "0.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NMF" version))
        (sha256
         (base32
-         "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
+         "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 418c6aff401b26c2c46f2619ef948806dcfadc38 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 11 Apr 2022 18:01:02 +0200
Subject: gnu: r-abn: Update to 2.7-0.

* gnu/packages/bioconductor.scm (r-abn): Update to 2.7-0.
[propagated-inputs]: Add r-graph.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 46ac053a27..04328c6876 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14209,20 +14209,21 @@ (define-public r-ldheatmap
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "2.6-0")
+    (version "2.7-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "0fr5pyc43hly5ry5bbygibbh9mnql7vl4r5qz42d0ry4hahyxa4w"))))
+         "13i2f4lw1rzj89bp31sn03prq1bqj7bsxwdr8z2ql02yqks9phg0"))))
     (build-system r-build-system)
     (inputs
      (list gsl))
     (propagated-inputs
      (list r-doparallel
            r-foreach
+           r-graph
            r-lme4
            r-nnet
            r-rcpp
-- 
cgit v1.2.3


From 855097683230b756ba28636bed03ce904b6f3589 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 12 Apr 2022 11:37:57 +0200
Subject: gnu: r-rbowtie: Fix build on architectures other than x86_64.

* gnu/packages/bioconductor.scm (r-rbowtie)[arguments]: Disable use of popcnt
on systems other than x86_64.
---
 gnu/packages/bioconductor.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 04328c6876..803437a033 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9677,6 +9677,18 @@ (define-public r-rbowtie
          "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       ;; Disable unsupported `popcnt' instructions on
+       ;; architectures other than x86_64
+       ,(if (string-prefix? "x86_64"
+                            (or (%current-target-system)
+                                (%current-system)))
+            '%standard-phases
+            '(modify-phases %standard-phases
+               (add-after 'unpack 'patch-sources
+                 (lambda _
+                   (setenv "POPCNT_CAPABILITY" "0")))))))
     (inputs (list zlib))
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From f6bc281cd7ffea91764ecfc63aa57b533c884f97 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 06:55:20 +0200
Subject: gnu: r-tricycle: Move out of annotation packages.

* gnu/packages/bioconductor.scm (r-tricycle): Move definition out of the
section containing annotation packages.
---
 gnu/packages/bioconductor.scm | 74 +++++++++++++++++++++----------------------
 1 file changed, 37 insertions(+), 37 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 803437a033..d3b5678343 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -775,43 +775,6 @@ (define-public r-ensdb-mmusculus-v79
 Ensembl.")
     (license license:artistic2.0)))
 
-(define-public r-tricycle
-  (package
-    (name "r-tricycle")
-    (version "1.2.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "tricycle" version))
-              (sha256
-               (base32
-                "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r"))))
-    (properties `((upstream-name . "tricycle")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-annotationdbi
-                             r-circular
-                             r-dplyr
-                             r-genomicranges
-                             r-ggplot2
-                             r-iranges
-                             r-rcolorbrewer
-                             r-s4vectors
-                             r-scater
-                             r-scattermore
-                             r-singlecellexperiment
-                             r-summarizedexperiment))
-    (native-inputs (list r-knitr))
-    (home-page "https://github.com/hansenlab/tricycle")
-    (synopsis "Transferable representation and inference of cell cycle")
-    (description
-     "The package contains functions to infer and visualize cell cycle process
-using Single-cell RNA-Seq data.  It exploits the idea of transfer learning,
-projecting new data to the previous learned biologically interpretable space.
-The @code{tricycle} provides a pre-learned cell cycle space, which could be
-used to infer cell cycle time of human and mouse single cell samples.  In
-addition, it also offer functions to visualize cell cycle time on different
-embeddings and functions to build new reference.")
-    (license license:gpl3)))
-
 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
   (package
     (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
@@ -15424,6 +15387,43 @@ (define-public r-tcgabiolinks
 starburst plots) in order to easily develop complete analysis pipelines.")
     (license license:gpl3+)))
 
+(define-public r-tricycle
+  (package
+    (name "r-tricycle")
+    (version "1.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tricycle" version))
+              (sha256
+               (base32
+                "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r"))))
+    (properties `((upstream-name . "tricycle")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi
+                             r-circular
+                             r-dplyr
+                             r-genomicranges
+                             r-ggplot2
+                             r-iranges
+                             r-rcolorbrewer
+                             r-s4vectors
+                             r-scater
+                             r-scattermore
+                             r-singlecellexperiment
+                             r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hansenlab/tricycle")
+    (synopsis "Transferable representation and inference of cell cycle")
+    (description
+     "The package contains functions to infer and visualize cell cycle process
+using Single-cell RNA-Seq data.  It exploits the idea of transfer learning,
+projecting new data to the previous learned biologically interpretable space.
+The @code{tricycle} provides a pre-learned cell cycle space, which could be
+used to infer cell cycle time of human and mouse single cell samples.  In
+addition, it also offer functions to visualize cell cycle time on different
+embeddings and functions to build new reference.")
+    (license license:gpl3)))
+
 (define-public r-tximeta
   (package
     (name "r-tximeta")
-- 
cgit v1.2.3


From ac67d0a4676679ab9d85a679176154b85451b05a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:49 +0200
Subject: gnu: r-annotationhub: Update to 3.2.2.

* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.2.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d3b5678343..61f2ad1dbb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2402,14 +2402,14 @@ (define-public r-annotationforge
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "3.2.0")
+    (version "3.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng"))))
+         "08dk4h07gpi3rk9s80wrbx2ww2chj688qzbwlx8n4dz788lqbfz8"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e4816bcaeda2d802b46aafd62b4780a1187faec1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:57 +0200
Subject: gnu: r-biomart: Update to 2.50.3.

* gnu/packages/bioconductor.scm (r-biomart): Update to 2.50.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 61f2ad1dbb..344a790cfd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2519,13 +2519,13 @@ (define-public r-biobase
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.50.1")
+    (version "2.50.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz"))))
+                "01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 9000c8acc20f9696a1c507800b0ab74374cae974 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:58 +0200
Subject: gnu: r-ensembldb: Update to 2.18.4.

* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.18.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 344a790cfd..ca579cc782 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3137,14 +3137,14 @@ (define-public r-edger
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.18.2")
+    (version "2.18.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx"))))
+         "1nsdcsghhh3ikv0hbn1aazdam7a6pqf1p6rz68ll2h6965kl4qzp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From 455636fecd4cf95179d7a166f6664d301d229d46 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:58 +0200
Subject: gnu: r-genomeinfodb: Update to 1.30.1.

* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.30.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ca579cc782..869971e57e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3327,13 +3327,13 @@ (define-public r-genomation
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.30.0")
+    (version "1.30.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns"))))
+                "1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 68c1c989b618d38a7ca3a4637502d93fb6c06127 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:58 +0200
Subject: gnu: r-genomicfeatures: Update to 1.46.5.

* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.46.5.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 869971e57e..2ad7fc88f5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3387,13 +3387,13 @@ (define-public r-genomicalignments
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.46.3")
+    (version "1.46.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk"))))
+                "1fhahqh87cikfrwqkm2z4nq3jyi530qvsbmf09j2hyhsm87hhrgg"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 78f7de977a438cb05435e110a4b750d6915e0836 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:58 +0200
Subject: gnu: r-limma: Update to 3.50.3.

* gnu/packages/bioconductor.scm (r-limma): Update to 3.50.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2ad7fc88f5..fb698b772b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3670,13 +3670,13 @@ (define-public r-keggrest
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.50.0")
+    (version "3.50.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy"))))
+                "1p46sif1aygmw2p8ifiylxrrbfbgvcsa0zp40nxlxawc7h56rybp"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
-- 
cgit v1.2.3


From e586613384dbde6ccd5ddfcdf31f0867ad05a654 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:58 +0200
Subject: gnu: r-mutationalpatterns: Update to 3.4.1.

* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.4.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fb698b772b..0068b4ae72 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3763,14 +3763,14 @@ (define-public r-motifrg
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "3.4.0")
+    (version "3.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl"))))
+         "0i6fq6736gvrqn45r7nrhl0ns45qwj1bl4yc6qlalw2g46mjxf6k"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From 06d13cf4b04ffa6954554cf47fbe77d17e410ba0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:59 +0200
Subject: gnu: r-msnbase: Update to 2.20.4.

* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.20.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0068b4ae72..83a890c004 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3809,14 +3809,14 @@ (define-public r-mutationalpatterns
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.20.1")
+    (version "2.20.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0ip614mdwisz2hlmyfgngysq1s3hajb88cgdmygfc8i6kyxjkjzl"))))
+         "0d3b0i154dyz1wvy2jwf5831bzbmalw7rzvxj8rd7658zjhghgzc"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 30027f837d00097146097c5c7cb01af3c65b3370 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:59 +0200
Subject: gnu: r-regioner: Update to 1.26.1.

* gnu/packages/bioconductor.scm (r-regioner): Update to 1.26.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 83a890c004..cf1c6d5b6a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4150,14 +4150,14 @@ (define-public r-rcas
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.26.0")
+    (version "1.26.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6"))))
+         "0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6dad28d2210d90eb8052261660194dddc3f07383 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:59 +0200
Subject: gnu: r-rhdf5: Update to 2.38.1.

* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.38.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cf1c6d5b6a..6cf02086c3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4231,13 +4231,13 @@ (define-public r-reportingtools
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.38.0")
+    (version "2.38.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg"))))
+                "1mlwp7bblhbpmd90sxj02zpq1q3fyg8v7ankyjb1y284xaymp02y"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rhdf5filters r-rhdf5lib))
-- 
cgit v1.2.3


From a3ddba54fdc459fa7f64cc04798c3ded41af4344 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:59 +0200
Subject: gnu: r-slingshot: Update to 2.2.1.

* gnu/packages/bioconductor.scm (r-slingshot): Update to 2.2.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6cf02086c3..956798bea2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4710,13 +4710,13 @@ (define-public r-trajectoryutils
 (define-public r-slingshot
   (package
    (name "r-slingshot")
-   (version "2.2.0")
+   (version "2.2.1")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "slingshot" version))
             (sha256
              (base32
-              "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa"))))
+              "10kjpmckhzjf41yfhzg7c8idqa9cxz33r4rza6rwihnqnw1liff3"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-igraph
-- 
cgit v1.2.3


From 43053e08da3f1cad8121b0b8ec1f1af9fad33f74 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:59 +0200
Subject: gnu: r-stringdb: Update to 2.6.5.

* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.6.5.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 956798bea2..2455db7ccf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4765,13 +4765,13 @@ (define-public r-stager
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-    (version "2.6.0")
+    (version "2.6.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "STRINGdb" version))
        (sha256
-        (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm"))))
+        (base32 "0n2r2zc2sx1a2a8wqqxz6z7i4ynaj18iwbwgif7469n13agji5mv"))))
     (properties `((upstream-name . "STRINGdb")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From cf46f2c33143e186f3013d94dc1ea74d977f19d2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:58:59 +0200
Subject: gnu: r-systempiper: Update to 2.0.8.

* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.0.8.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2455db7ccf..ff7e6d9ec3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4900,14 +4900,14 @@ (define-public r-sva
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.0.5")
+    (version "2.0.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf"))))
+         "0ajlw9yg6fha76rkkmsk5niq99s33k9437bkgi9whgh3pa6bkab2"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From f7d7ba36131bcf5025a1dc7a24a53790b7b8c1c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:00 +0200
Subject: gnu: r-diffbind: Update to 3.4.11.

* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.4.11.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ff7e6d9ec3..54ce7551b7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5455,14 +5455,14 @@ (define-public r-greylistchip
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.4.3")
+    (version "3.4.11")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj"))))
+         "1xprj3x3s3yh6fwsdcl4zgfbhn640422x1lhhrmvdr836jr8sxcj"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d625f52bca43eb8d7a281b2ce58440be65b464f3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:00 +0200
Subject: gnu: r-chippeakanno: Update to 3.28.1.

* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.28.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 54ce7551b7..17085b791d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5693,14 +5693,14 @@ (define-public r-codedepends
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.28.0")
+    (version "3.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b"))))
+         "0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 84c0ec875ca8e1f43ada53c0ffbb6926a7d48b88 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:00 +0200
Subject: gnu: r-destiny: Update to 3.8.1.

* gnu/packages/bioconductor.scm (r-destiny): Update to 3.8.1.
[native-inputs]: Add r-knitr.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 17085b791d..6011045a3d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6476,14 +6476,14 @@ (define-public r-biocsingular
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.8.0")
+    (version "3.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y"))))
+         "1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -6509,7 +6509,7 @@ (define-public r-destiny
            r-tidyselect
            r-vim))
     (native-inputs
-     (list r-nbconvertr)) ; for vignettes
+     (list r-knitr r-nbconvertr)) ; for vignettes
     (home-page "https://bioconductor.org/packages/destiny/")
     (synopsis "Create and plot diffusion maps")
     (description "This package provides tools to create and plot diffusion
-- 
cgit v1.2.3


From fe6a8b4338e4197f8a3e16359211c3a807e09432 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:00 +0200
Subject: gnu: r-karyoploter: Update to 1.20.3.

* gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.20.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6011045a3d..bb87008214 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6722,13 +6722,13 @@ (define-public r-ebseq
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.20.0")
+    (version "1.20.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq"))))
+                "0bcc1ln7602lrbm9wckgyfd9slsqiljjmymj28rfpax1n8rbq44m"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From f8a38e83809e5e717c03af773954a7ca7659cf8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:00 +0200
Subject: gnu: r-geoquery: Update to 2.62.2.

* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.62.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bb87008214..58d46ede8d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7254,14 +7254,14 @@ (define-public r-scone
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.62.1")
+    (version "2.62.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "0plmh4x37r848g6ilvl1x8cim90rp85gikfc5m8lgi2i4xkq7hbq"))))
+         "1hncr0p54qdg82a771yjjm4w1k2myrc26jzvci3g37mq7bgv3mxw"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 21037105ace009c4e96acce92dcdda84e8d765e1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:01 +0200
Subject: gnu: r-enrichplot: Update to 1.14.2.

* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.14.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 58d46ede8d..da9a69a746 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7970,14 +7970,14 @@ (define-public r-dose
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.14.1")
+    (version "1.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch"))))
+         "1rjiqmc32c9gxckgrgbypxpp0m8y0kahvhzvjzymda25xp8zqjs2"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
-- 
cgit v1.2.3


From e129f579f514531238d1601435bbd24a82c4ae3e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:01 +0200
Subject: gnu: r-clusterprofiler: Update to 4.2.2.

* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.2.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index da9a69a746..a9d283c321 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8008,14 +8008,14 @@ (define-public r-enrichplot
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "4.2.1")
+    (version "4.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4"))))
+         "1y8ay3fxvcc7a7yqvfc95jfn800ikvs56j17byyp6v08w2j00y76"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 88ed3fc340e86c20a0d2fe34204b66273b63b18e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:01 +0200
Subject: gnu: r-genomicscores: Update to 2.6.1.

* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.6.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a9d283c321..734e198910 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8551,14 +8551,14 @@ (define-public r-motifstack
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.6.0")
+    (version "2.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls"))))
+         "17v2v7aklljy17nivwmani2jxkbffqs2yr38hlspjlvgpidpf9ln"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6f2d89fb4036d94093e00b712a6b9708079e1cf8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:01 +0200
Subject: gnu: r-atacseqqc: Update to 1.18.1.

* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.18.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 734e198910..f953e567ea 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8588,14 +8588,14 @@ (define-public r-genomicscores
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn"))))
+         "1jmlialnhs9df1hv6l4qk2c4qjyjbz9mdj8vr52ms8vlxlxplz6c"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 5576a98b6a70daa8f0f1a150c41dc30534cf6feb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:01 +0200
Subject: gnu: r-massspecwavelet: Update to 1.60.1.

* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.60.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f953e567ea..887cb9aef9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9253,14 +9253,14 @@ (define-public r-xbseq
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.60.0")
+    (version "1.60.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4"))))
+         "00irq3i5kfck7rnm8ll7rqhqfpp3bisv2h8is50a7wbd7480z7ij"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From b446be46ba578b7dab61a9188cffd91186fd77a0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:02 +0200
Subject: gnu: r-biocfilecache: Update to 2.2.1.

* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.2.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 887cb9aef9..a741993317 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9567,14 +9567,14 @@ (define-public r-arrmnormalization
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1"))))
+         "0gaj0z6dk2p2vhvqz685xwd5q2mkvpimh2493p3w04s2rlsvi3jb"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0c478f50f2981554fd0de7fbe72afd9101511f7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:02 +0200
Subject: gnu: r-birewire: Update to 3.26.5.

* gnu/packages/bioconductor.scm (r-birewire): Update to 3.26.5.
[propagated-inputs]: Remove r-tsne; add r-rtsne.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a741993317..071d845615 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9832,18 +9832,18 @@ (define-public r-rqc
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.26.0")
+    (version "3.26.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w"))))
+         "041i5d08bsc5jqx3309fixjacizs4yi992cwazxghm8mrk3kicbr"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-igraph r-matrix r-slam r-tsne))
+     (list r-igraph r-matrix r-rtsne r-slam))
     (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
     (synopsis "Tools for randomization of bipartite graphs")
     (description
-- 
cgit v1.2.3


From cb304000977fd633f7d2c8b1062866875b33885b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:02 +0200
Subject: gnu: r-ropls: Update to 1.26.4.

* gnu/packages/bioconductor.scm (r-ropls): Update to 1.26.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 071d845615..d63f6ef527 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9922,14 +9922,14 @@ (define-public r-multidataset
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.26.0")
+    (version "1.26.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05"))))
+         "19f3wd55860x959h5n7mrivyjdas5b3jmx74lf24xnx23g26f8rn"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-multidataset))
-- 
cgit v1.2.3


From 0861d4fff56697cc68b054ab080976767f48a1a7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:02 +0200
Subject: gnu: r-rsubread: Update to 2.8.2.

* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.8.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d63f6ef527..1ca6f90612 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10029,14 +10029,14 @@ (define-public r-annotatr
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.8.1")
+    (version "2.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn"))))
+         "078zcchw9xl6vs2wihzzji349vq0m1a039m86jdlvb7nc3i1imfk"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs (list zlib))
-- 
cgit v1.2.3


From 9950ed71fcbb107a8c9222fe00c216ea1e936851 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:02 +0200
Subject: gnu: r-cytolib: Update to 2.6.2.

* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.6.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1ca6f90612..ef58ee0754 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10147,14 +10147,14 @@ (define-public r-cycombine
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.6.1")
+    (version "2.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9"))))
+         "0ycr4wmkfi0rvzwicblkfjgppk72gwwpim0rfiz1s44lycsf4py5"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From eadb1f53e9511f4d7ce2b1dcfec58adcb8324522 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:03 +0200
Subject: gnu: r-variancepartition: Update to 1.24.1.

* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.24.1.
[propagated-inputs]: Add r-aod, r-rdpack, and r-rhpcblasctl.
---
 gnu/packages/bioconductor.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ef58ee0754..c787e446a1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11461,19 +11461,20 @@ (define-public r-wavetiling
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.24.0")
+    (version "1.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw"))))
+         "14aki7d9xl4rhhzv3cl09mbj1q7xhxg69s4kzms9hfv3cqjryqd7"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-biobase
+     (list r-aod
+           r-biobase
            r-biocparallel
            r-doparallel
            r-foreach
@@ -11487,7 +11488,9 @@ (define-public r-variancepartition
            r-matrix
            r-pbkrtest
            r-progress
+           r-rdpack
            r-reshape2
+           r-rhpcblasctl
            r-rlang
            r-scales))
     (native-inputs
-- 
cgit v1.2.3


From c9e925d4443cbd879a3f41d0f57345ec311b18b6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:03 +0200
Subject: gnu: r-universalmotif: Update to 1.12.4.

* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.12.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c787e446a1..d4d570cf26 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11563,14 +11563,14 @@ (define-public r-unifiedwmwqpcr
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.12.2")
+    (version "1.12.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg"))))
+         "01skcvzd815m3c15ka2pk7z6bggc4l8bhvaf4z9v95i36k4mn5zd"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 51ddaf48e8b6cac7cf7f7c38be8f94a824814140 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:03 +0200
Subject: gnu: r-experimenthub: Update to 2.2.1.

* gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.2.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d4d570cf26..f0846bf1f8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12316,14 +12316,14 @@ (define-public r-biocviews
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq"))))
+         "0lvd6hyqdfsn5ji714v46qdrb8vr1y38lv0pgw8priab0hpqrbm5"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 2a71a7b961ffa6e89c6509455b70027a47e1222c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:03 +0200
Subject: gnu: r-s4vectors: Update to 0.32.4.

* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.32.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f0846bf1f8..55c8dfb6f0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12872,13 +12872,13 @@ (define-public r-preprocesscore
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.32.3")
+    (version "0.32.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw"))))
+                "17dvypxcwp8c7ih23hi2366110by6zq1mjgxkmlbiklzachg9780"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 40735701a852acee27fef6756254120e37f437d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:03 +0200
Subject: gnu: r-singler: Update to 1.8.1.

* gnu/packages/bioconductor.scm (r-singler): Update to 1.8.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55c8dfb6f0..dc05a94cff 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13396,13 +13396,13 @@ (define-public r-singlecellexperiment
 (define-public r-singler
   (package
     (name "r-singler")
-    (version "1.8.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleR" version))
        (sha256
-        (base32 "19lsn3cpghkhfbx4jqgbwwrnacrl7vj3r91ymd1gk02c9pn5dmci"))))
+        (base32 "0j0h6ipm65wv38qx40z16h01mfirpshfn4lhlwlg2nri4vmihlpi"))))
     (properties `((upstream-name . "SingleR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3e07fbf32af4211d746e1e29a2950ac755db4fb2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:03 +0200
Subject: gnu: r-mscoreutils: Update to 1.6.2.

* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.6.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dc05a94cff..23953c6e76 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13608,14 +13608,14 @@ (define-public r-delayedmatrixstats
 (define-public r-mscoreutils
   (package
     (name "r-mscoreutils")
-    (version "1.6.0")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsCoreUtils" version))
        (sha256
         (base32
-         "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv"))))
+         "0614a830gf676ck8j5lkm04158pfvhjb61p3xfdd69gg3d44mk1d"))))
     (properties `((upstream-name . "MsCoreUtils")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3c7e190eeac9ae29eee3dfcf3d58d7a5c8749c9a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:04 +0200
Subject: gnu: r-catalyst: Update to 1.18.1.

* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.18.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 23953c6e76..400d91fc37 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13752,14 +13752,14 @@ (define-public r-msmstests
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi"))))
+            "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c7cb92e49486ac78b4e9b00885ac18e47be8aa16 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:04 +0200
Subject: gnu: r-gviz: Update to 1.38.4.

* gnu/packages/bioconductor.scm (r-gviz): Update to 1.38.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 400d91fc37..8712e54e2a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14018,14 +14018,14 @@ (define-public r-gqtlstats
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.38.0")
+    (version "1.38.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8"))))
+         "14qybi5b3h9z5b0m127jf7z695amf612rh5wq2g2n1yirfhzbdja"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 2def20d3ae0f562f5c02f3e91e5f4c372c4be602 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:04 +0200
Subject: gnu: r-bgeedb: Update to 2.20.1.

* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.20.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8712e54e2a..bd0784df5d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14534,14 +14534,14 @@ (define-public r-bgeecall
 (define-public r-bgeedb
   (package
     (name "r-bgeedb")
-    (version "2.20.0")
+    (version "2.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeDB" version))
        (sha256
         (base32
-         "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk"))))
+         "0mrw7fwjx8k0a5c3iw2j94h1yn5pkvqil7fbzih9xiafnpbn374m"))))
     (properties `((upstream-name . "BgeeDB")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 5acc1253055747baf1be09fdee8c5141cb99b38c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:04 +0200
Subject: gnu: r-omnipathr: Update to 3.2.8.

* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.2.8.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bd0784df5d..18ab990b04 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15235,13 +15235,13 @@ (define-public r-dmrseq
 (define-public r-omnipathr
   (package
     (name "r-omnipathr")
-    (version "3.2.0")
+    (version "3.2.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OmnipathR" version))
        (sha256
-        (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8"))))
+        (base32 "0vr16ar3rbjsfw4qz2g86lbhvmqwgq0vcahc6vrc4d9rdjxwg6sb"))))
     (properties `((upstream-name . "OmnipathR")))
     (build-system r-build-system)
     (arguments
-- 
cgit v1.2.3


From d85146c9df3f521a0207a79cb3baccceffe5ac42 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 10:59:04 +0200
Subject: gnu: r-tcgabiolinks: Update to 2.22.4.

* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.22.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 18ab990b04..b492214971 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15338,13 +15338,13 @@ (define-public r-biscuiteer
 (define-public r-tcgabiolinks
   (package
     (name "r-tcgabiolinks")
-    (version "2.22.2")
+    (version "2.22.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TCGAbiolinks" version))
        (sha256
-        (base32 "0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc"))))
+        (base32 "071wz6dm6dypbfzvxd6j67l1iawlb6d5sfzq871zh06fzaxjm332"))))
     (properties `((upstream-name . "TCGAbiolinks")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 7d990e775e76c0a898c7d4b53691d1932fc0e6eb Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 13 Apr 2022 13:21:03 +0200
Subject: gnu: r-catalyst: Update description.

* gnu/packages/bioconductor.scm (r-catalyst)[description]: Add Texinfo markup
and clarify a sentence.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++------------
 1 file changed, 17 insertions(+), 12 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b492214971..1401053570 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13791,20 +13791,25 @@ (define-public r-catalyst
             r-summarizedexperiment))
     (native-inputs
      (list r-knitr))
-    (home-page
-      "https://github.com/HelenaLC/CATALYST")
+    (home-page "https://github.com/HelenaLC/CATALYST")
     (synopsis "Cytometry data analysis tools")
     (description
-      "This package is Cytometry dATa anALYSis Tools (CATALYST).  Mass
-cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
-reporters to label antibodies, thereby substantially decreasing spectral
-overlap and allowing for examination of over 50 parameters at the single cell
-level.  While spectral overlap is significantly less pronounced in CyTOF than
-flow cytometry, spillover due to detection sensitivity, isotopic impurities,
-and oxide formation can impede data interpretability.  We designed
-CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
-preprocessing of cytometry data, including i) normalization using bead
-standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
+     "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST).  Mass
+cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
+isotopes rather than fluorescent tags as reporters to label antibodies,
+thereby substantially decreasing spectral overlap and allowing for examination
+of over 50 parameters at the single cell level.  While spectral overlap is
+significantly less pronounced in CyTOF than flow cytometry, spillover due to
+detection sensitivity, isotopic impurities, and oxide formation can impede
+data interpretability.  @code{CATALYST} was designed to provide a pipeline for
+preprocessing of cytometry data, including:
+
+@enumerate
+@item normalization using bead standards;
+@item single-cell deconvolution;
+@item bead-based compensation.
+@end enumerate
+")
     (license license:gpl2+)))
 
 (define-public r-erma
-- 
cgit v1.2.3


From 839241501ad571e669471a711efb9172db40f708 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 13 Apr 2022 14:04:42 +0200
Subject: gnu: Add r-ace.

* gnu/packages/bioconductor.scm (r-ace): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1401053570..bae472c8ac 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11608,6 +11608,35 @@ (define-public r-universalmotif
 motifs, and others.")
     (license license:gpl3)))
 
+(define-public r-ace
+  (package
+    (name "r-ace")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ACE" version))
+              (sha256
+               (base32
+                "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6"))))
+    (properties `((upstream-name . "ACE")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/tgac-vumc/ACE")
+    (synopsis
+     "Absolute copy number estimation from low-coverage whole genome sequencing")
+    (description
+     "This package uses segmented copy number data to estimate tumor cell
+percentage and produce copy number plots displaying absolute copy numbers.  For
+this it uses segmented data from the @code{QDNAseq} package, which in turn uses
+a number of dependencies to turn mapped reads into segmented data.  @code{ACE}
+will run @code{QDNAseq} or use its output rds-file of segmented data.  It will
+subsequently run through all samples in the object(s), for which it will create
+individual subdirectories.  For each sample, it will calculate how well the
+segments fit (the relative error) to integer copy numbers for each percentage
+of @dfn{tumor cells} (cells with divergent segments).")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
 ;; it here.
 (define-public r-activedriverwgs
-- 
cgit v1.2.3


From 08df30f232afc1fc1ae7fb3c9889b5ad96bc5dea Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 13 Apr 2022 14:21:38 +0200
Subject: gnu: Add r-acgh.

* gnu/packages/bioconductor.scm (r-acgh): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bae472c8ac..d3e16cd859 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11637,6 +11637,30 @@ (define-public r-ace
 of @dfn{tumor cells} (cells with divergent segments).")
     (license license:gpl2)))
 
+(define-public r-acgh
+  (package
+    (name "r-acgh")
+    (version "1.72.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "aCGH" version))
+              (sha256
+               (base32
+                "1r1q6iq3g7svfn5m4jxlxp413djb40mvf6lh595y86sgwav5k6l4"))))
+    (properties `((upstream-name . "aCGH")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
+    (home-page "https://bioconductor.org/packages/aCGH")
+    (synopsis
+     "Classes and functions for array comparative genomic hybridization data")
+    (description
+     "This package provides functions for reading
+@dfn{array comparative genomic hybridization} (aCGH) data from image analysis
+output files and clone information files, creation of @code{aCGH} objects for
+storing these data.  Basic methods are accessing/replacing, subsetting,
+printing and plotting @code{aCGH} objects.")
+    (license license:gpl2)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
 ;; it here.
 (define-public r-activedriverwgs
-- 
cgit v1.2.3


From 55be5fc400ed30cceca279de13dcbe270b60fee4 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 13 Apr 2022 16:12:58 +0200
Subject: gnu: Add r-acme.

* gnu/packages/bioconductor.scm (r-acme): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d3e16cd859..8664f1139f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11661,6 +11661,33 @@ (define-public r-acgh
 printing and plotting @code{aCGH} objects.")
     (license license:gpl2)))
 
+(define-public r-acme
+  (package
+    (name "r-acme")
+    (version "2.50.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ACME" version))
+              (sha256
+               (base32
+                "0h4bqbbqcwc938q7lysk5l35f64xz9d1bsniv2wshmlr4rr0zpcg"))))
+    (properties `((upstream-name . "ACME")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-biocgenerics))
+    (home-page "https://bioconductor.org/packages/aCGH/")
+    (synopsis "Calculating microarray enrichment")
+    (description
+     "This package implements @dfn{algorithms for calculating microarray
+enrichment} (ACME), and it is a set of tools for analysing tiling array of
+@dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
+DNAse hypersensitivity, or other experiments that result in regions of the
+genome showing enrichment.  It does not rely on a specific array technology
+(although the array should be a tiling array), is very general (can be applied
+in experiments resulting in regions of enrichment), and is very insensitive to
+array noise or normalization methods.  It is also very fast and can be applied
+on whole-genome tiling array experiments quite easily with enough memory.")
+    (license license:gpl2+)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
 ;; it here.
 (define-public r-activedriverwgs
-- 
cgit v1.2.3


From dd9d26bce626cb2900910f1706de38c47a52915a Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 11 Apr 2022 16:29:16 +0200
Subject: gnu: Add r-wppi.

* gnu/packages/bioconductor.scm (r-wppi): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8664f1139f..786e79b931 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9315,6 +9315,47 @@ (define-public r-xcms
 data for high-throughput, untargeted analyte profiling.")
     (license license:gpl2+)))
 
+(define-public r-wppi
+  (package
+    (name "r-wppi")
+    (version "1.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "wppi" version))
+              (sha256
+               (base32
+                "1spwa8p6w3pyw21dvd1lrhcz1sphdsmsd408jv55ss9nbgvgrp23"))))
+    (properties `((upstream-name . "wppi")))
+    (build-system r-build-system)
+    ;; This is necessary because omnipathr attempts to write a configuration
+    ;; file to HOME.
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs (list r-dplyr
+                             r-igraph
+                             r-logger
+                             r-magrittr
+                             r-matrix
+                             r-omnipathr
+                             r-progress
+                             r-purrr
+                             r-rcurl
+                             r-rlang
+                             r-tibble
+                             r-tidyr))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/AnaGalhoz37/wppi")
+    (synopsis "Weighting protein-protein interactions")
+    (description
+     "This package predicts functional relevance of protein-protein
+interactions based on functional annotations such as Human Protein Ontology
+and Gene Ontology, and prioritizes genes based on network topology, functional
+scores and a path search algorithm.")
+    (license license:expat)))
+
 (define-public r-wrench
   (package
     (name "r-wrench")
-- 
cgit v1.2.3


From 1b2b1c30e2adec2afa868badbada45d7d7cd755d Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 13 Apr 2022 00:30:47 +0200
Subject: gnu: Add r-acde.

* gnu/packages/bioconductor.scm (r-acde): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 786e79b931..6559e69711 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11729,6 +11729,31 @@ (define-public r-acme
 on whole-genome tiling array experiments quite easily with enough memory.")
     (license license:gpl2+)))
 
+(define-public r-acde
+  (package
+    (name "r-acde")
+    (version "1.24.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "acde" version))
+              (sha256
+               (base32
+                "13ks87am73m3bjn9ljapxml2a9cxdpgv9flwvly8aqmi3ndxyqi6"))))
+    (properties `((upstream-name . "acde")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-boot))
+    (home-page "https://bioconductor.org/packages/acde")
+    (synopsis
+     "Identification of differentially expressed genes with artificial components")
+    (description
+     "This package provides a multivariate inferential analysis method for
+detecting differentially expressed genes in gene expression data.  It uses
+artificial components, close to the data's principal components but with an
+exact interpretation in terms of differential genetic expression, to identify
+differentially expressed genes while controlling the @dfn{false discovery
+rate} (FDR).")
+    (license license:gpl3)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
 ;; it here.
 (define-public r-activedriverwgs
-- 
cgit v1.2.3


From a436582124a4e4d1e075bb8ba5eb6a18fbfd8145 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 12 Apr 2022 18:15:09 +0200
Subject: gnu: Add r-abarray.

* gnu/packages/bioconductor.scm (r-abarray): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6559e69711..69ffdbe79b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1102,6 +1102,32 @@ (define-public r-abadata
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
+(define-public r-abarray
+  (package
+    (name "r-abarray")
+    (version "1.62.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ABarray" version))
+              (sha256
+               (base32
+                "0yh7jmkwdg3kmm98ii0cxbla3s5bwy84fpg6xcpggsrriwzwfb5k"))))
+    (properties `((upstream-name . "ABarray")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-multtest))
+    (home-page "https://bioconductor.org/packages/ABarray")
+    (synopsis
+     "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
+    (description
+     "The package @code{ABarray} is designed to work with Applied Biosystems
+whole genome microarray platform, as well as any other platform whose data can
+be transformed into expression data matrix.  Functions include data
+preprocessing, filtering, control probe analysis, statistical analysis in one
+single function.  A @dfn{graphical user interface} (GUI) is also provided.  The
+raw data, processed data, graphics output and statistical results are organized
+into folders according to the analysis settings used.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")
-- 
cgit v1.2.3


From cab66570947a8d6fc1acd380151e91a65cf4a6bb Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 12 Apr 2022 23:57:55 +0200
Subject: gnu: Add r-absseq.

* gnu/packages/bioconductor.scm (r-absseq): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 69ffdbe79b..e6f462b697 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1128,6 +1128,35 @@ (define-public r-abarray
 into folders according to the analysis settings used.")
     (license license:gpl2+)))
 
+(define-public r-absseq
+  (package
+    (name "r-absseq")
+    (version "1.48.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ABSSeq" version))
+              (sha256
+               (base32
+                "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650"))))
+    (properties `((upstream-name . "ABSSeq")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-limma r-locfit))
+    (home-page "https://bioconductor.org/packages/ABSSeq")
+    (synopsis
+     "RNA-Seq analysis based on modelling absolute expression differences")
+    (description
+     "This package implements a new RNA-Seq analysis method and integrates two
+modules: a basic model for pairwise comparison and a linear model for complex
+design.  RNA-Seq quantifies gene expression with reads count, which usually
+consists of conditions (or treatments) and several replicates for each
+condition.  This software infers differential expression directly by the
+counts difference between conditions.  It assumes that the sum counts
+difference between conditions follow a negative binomial distribution.  In
+addition, @code{ABSSeq} moderates the fold-changes by two steps: the
+expression level and gene-specific dispersion, that might facilitate the gene
+ranking by fold-change and visualization.")
+    (license license:gpl3+)))
+
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")
-- 
cgit v1.2.3


From 67941709e21c7f14bec0924aa6a893840c70ec68 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 13:31:33 +0200
Subject: gnu: r-aneufinder: Move to packages section.

* gnu/packages/bioconductor.scm (r-aneufinder): Move this definition out of
the section for Bioconductor experiments packages.
---
 gnu/packages/bioconductor.scm | 84 +++++++++++++++++++++----------------------
 1 file changed, 42 insertions(+), 42 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e6f462b697..5a20fbbc64 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1173,48 +1173,6 @@ (define-public r-aneufinderdata
    (description "This package contains data used by @code{AneuFinder}.")
    (license license:artistic2.0)))
 
-(define-public r-aneufinder
-  (package
-    (name "r-aneufinder")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "AneuFinder" version))
-              (sha256
-               (base32
-                "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0"))))
-    (build-system r-build-system)
-    (native-inputs
-     (list r-knitr))
-    (propagated-inputs
-     (list r-genomicranges
-           r-aneufinderdata
-           r-ecp
-           r-foreach
-           r-doparallel
-           r-biocgenerics
-           r-s4vectors
-           r-genomeinfodb
-           r-iranges
-           r-rsamtools
-           r-bamsignals
-           r-dnacopy
-           r-biostrings
-           r-genomicalignments
-           r-ggplot2
-           r-reshape2
-           r-ggdendro
-           r-ggrepel
-           r-reordercluster
-           r-mclust
-           r-cowplot))
-    (home-page "https://bioconductor.org/packages/AneuFinder/")
-    (synopsis "Copy number variation analysis in single-cell-sequencing data")
-    (description "This package implements functions for copy number variant
-calling, plotting, export and analysis from whole-genome single cell
-sequencing data.")
-    (license license:artistic2.0)))
-
 (define-public r-arrmdata
   (package
     (name "r-arrmdata")
@@ -1587,6 +1545,48 @@ (define-public r-tcgabiolinksgui-data
 
 ;;; Packages
 
+(define-public r-aneufinder
+  (package
+    (name "r-aneufinder")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AneuFinder" version))
+              (sha256
+               (base32
+                "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0"))))
+    (build-system r-build-system)
+    (native-inputs
+     (list r-knitr))
+    (propagated-inputs
+     (list r-genomicranges
+           r-aneufinderdata
+           r-ecp
+           r-foreach
+           r-doparallel
+           r-biocgenerics
+           r-s4vectors
+           r-genomeinfodb
+           r-iranges
+           r-rsamtools
+           r-bamsignals
+           r-dnacopy
+           r-biostrings
+           r-genomicalignments
+           r-ggplot2
+           r-reshape2
+           r-ggdendro
+           r-ggrepel
+           r-reordercluster
+           r-mclust
+           r-cowplot))
+    (home-page "https://bioconductor.org/packages/AneuFinder/")
+    (synopsis "Copy number variation analysis in single-cell-sequencing data")
+    (description "This package implements functions for copy number variant
+calling, plotting, export and analysis from whole-genome single cell
+sequencing data.")
+    (license license:artistic2.0)))
+
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-- 
cgit v1.2.3


From ed3697c040da3baf03a94fdac98e6a1a188c13d6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 13:32:52 +0200
Subject: gnu: r-abarray: Move out of experiments section.

* gnu/packages/bioconductor.scm (r-abarray): Move definition out of
experiments section.
---
 gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++----------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5a20fbbc64..61fa6bfde2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1102,32 +1102,6 @@ (define-public r-abadata
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
-(define-public r-abarray
-  (package
-    (name "r-abarray")
-    (version "1.62.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "ABarray" version))
-              (sha256
-               (base32
-                "0yh7jmkwdg3kmm98ii0cxbla3s5bwy84fpg6xcpggsrriwzwfb5k"))))
-    (properties `((upstream-name . "ABarray")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-biobase r-multtest))
-    (home-page "https://bioconductor.org/packages/ABarray")
-    (synopsis
-     "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
-    (description
-     "The package @code{ABarray} is designed to work with Applied Biosystems
-whole genome microarray platform, as well as any other platform whose data can
-be transformed into expression data matrix.  Functions include data
-preprocessing, filtering, control probe analysis, statistical analysis in one
-single function.  A @dfn{graphical user interface} (GUI) is also provided.  The
-raw data, processed data, graphics output and statistical results are organized
-into folders according to the analysis settings used.")
-    (license license:gpl2+)))
-
 (define-public r-absseq
   (package
     (name "r-absseq")
@@ -1545,6 +1519,32 @@ (define-public r-tcgabiolinksgui-data
 
 ;;; Packages
 
+(define-public r-abarray
+  (package
+    (name "r-abarray")
+    (version "1.62.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ABarray" version))
+              (sha256
+               (base32
+                "0yh7jmkwdg3kmm98ii0cxbla3s5bwy84fpg6xcpggsrriwzwfb5k"))))
+    (properties `((upstream-name . "ABarray")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-multtest))
+    (home-page "https://bioconductor.org/packages/ABarray")
+    (synopsis
+     "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
+    (description
+     "The package @code{ABarray} is designed to work with Applied Biosystems
+whole genome microarray platform, as well as any other platform whose data can
+be transformed into expression data matrix.  Functions include data
+preprocessing, filtering, control probe analysis, statistical analysis in one
+single function.  A @dfn{graphical user interface} (GUI) is also provided.  The
+raw data, processed data, graphics output and statistical results are organized
+into folders according to the analysis settings used.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From aafd0d2309a7f27dc0f724f682c4faede41cf6c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 13:34:11 +0200
Subject: gnu: r-absseq: Move out of experiments section.

* gnu/packages/bioconductor.scm (r-absseq): Move definition out of experiments
section.
---
 gnu/packages/bioconductor.scm | 58 +++++++++++++++++++++----------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 61fa6bfde2..ecb188a84f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1102,35 +1102,6 @@ (define-public r-abadata
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
-(define-public r-absseq
-  (package
-    (name "r-absseq")
-    (version "1.48.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "ABSSeq" version))
-              (sha256
-               (base32
-                "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650"))))
-    (properties `((upstream-name . "ABSSeq")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-limma r-locfit))
-    (home-page "https://bioconductor.org/packages/ABSSeq")
-    (synopsis
-     "RNA-Seq analysis based on modelling absolute expression differences")
-    (description
-     "This package implements a new RNA-Seq analysis method and integrates two
-modules: a basic model for pairwise comparison and a linear model for complex
-design.  RNA-Seq quantifies gene expression with reads count, which usually
-consists of conditions (or treatments) and several replicates for each
-condition.  This software infers differential expression directly by the
-counts difference between conditions.  It assumes that the sum counts
-difference between conditions follow a negative binomial distribution.  In
-addition, @code{ABSSeq} moderates the fold-changes by two steps: the
-expression level and gene-specific dispersion, that might facilitate the gene
-ranking by fold-change and visualization.")
-    (license license:gpl3+)))
-
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")
@@ -1545,6 +1516,35 @@ (define-public r-abarray
 into folders according to the analysis settings used.")
     (license license:gpl2+)))
 
+(define-public r-absseq
+  (package
+    (name "r-absseq")
+    (version "1.48.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ABSSeq" version))
+              (sha256
+               (base32
+                "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650"))))
+    (properties `((upstream-name . "ABSSeq")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-limma r-locfit))
+    (home-page "https://bioconductor.org/packages/ABSSeq")
+    (synopsis
+     "RNA-Seq analysis based on modelling absolute expression differences")
+    (description
+     "This package implements a new RNA-Seq analysis method and integrates two
+modules: a basic model for pairwise comparison and a linear model for complex
+design.  RNA-Seq quantifies gene expression with reads count, which usually
+consists of conditions (or treatments) and several replicates for each
+condition.  This software infers differential expression directly by the
+counts difference between conditions.  It assumes that the sum counts
+difference between conditions follow a negative binomial distribution.  In
+addition, @code{ABSSeq} moderates the fold-changes by two steps: the
+expression level and gene-specific dispersion, that might facilitate the gene
+ranking by fold-change and visualization.")
+    (license license:gpl3+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From c8a6e4abbc4f279f919017d238576cf8724e9456 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 13:35:22 +0200
Subject: gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics).

* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
---
 gnu/packages/bioconductor.scm   | 28 ----------------------------
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 28 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ecb188a84f..f795b6ad9c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1211,34 +1211,6 @@ (define-public r-chromstardata
 chromstaR package.")
     (license license:gpl3)))
 
-(define-public r-chromvarmotifs
-  (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
-        (revision "1"))
-    (package
-      (name "r-chromvarmotifs")
-      (version (git-version "0.2.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/GreenleafLab/chromVARmotifs")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q"))))
-      (properties `((upstream-name . "chromVARmotifs")))
-      (build-system r-build-system)
-      (propagated-inputs
-       `(("r-tfbstools" ,r-tfbstools)))
-      (home-page "https://github.com/GreenleafLab/chromVARmotifs")
-      (synopsis "Stores motif collections for use with motifmatchr or chromVAR")
-      (description
-       "This package stores motif collections as lists of @dfn{position
-frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools}
-package for use in R with packages like @code{motifmatchr} or
-@code{chromVAR}.")
-      (license license:expat))))
-
 (define-public r-copyhelper
   (package
     (name "r-copyhelper")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e3bbdaa380..b838c2dbfa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8981,6 +8981,34 @@ (define-public variant-tools
 manipulate and analyze genetic variants.")
     (license license:gpl3+)))
 
+(define-public r-chromvarmotifs
+  (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
+        (revision "1"))
+    (package
+      (name "r-chromvarmotifs")
+      (version (git-version "0.2.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/GreenleafLab/chromVARmotifs")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q"))))
+      (properties `((upstream-name . "chromVARmotifs")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-tfbstools" ,r-tfbstools)))
+      (home-page "https://github.com/GreenleafLab/chromVARmotifs")
+      (synopsis "Stores motif collections for use with motifmatchr or chromVAR")
+      (description
+       "This package stores motif collections as lists of @dfn{position
+frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools}
+package for use in R with packages like @code{motifmatchr} or
+@code{chromVAR}.")
+      (license license:expat))))
+
 (define-public r-raremetals2
   (package
     (name "r-raremetals2")
-- 
cgit v1.2.3


From 03009f2a2bb5c94e94735d2ff9314502412066a4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 13:37:23 +0200
Subject: gnu: r-snplocs-hsapiens-dbsnp144-grch37: Move to annotation section.

* gnu/packages/bioconductor.scm (r-snplocs-hsapiens-dbsnp144-grch37): Move
this variable up to the annotation section.
---
 gnu/packages/bioconductor.scm | 76 +++++++++++++++++++++----------------------
 1 file changed, 38 insertions(+), 38 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f795b6ad9c..094bd0d907 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -775,6 +775,44 @@ (define-public r-ensdb-mmusculus-v79
 Ensembl.")
     (license license:artistic2.0)))
 
+(define-public r-snplocs-hsapiens-dbsnp144-grch37
+  (package
+    (name "r-snplocs-hsapiens-dbsnp144-grch37")
+    (version "0.99.20")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
+                                     version 'annotation))
+              (sha256
+               (base32
+                "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
+    (build-system r-build-system)
+    ;; As this package provides little more than a very large data file it
+    ;; doesn't make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (propagated-inputs
+     (list r-biocgenerics
+           r-s4vectors
+           r-iranges
+           r-genomeinfodb
+           r-genomicranges
+           r-bsgenome
+           r-biostrings))
+    (home-page
+     "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
+    (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
+    (description "This package provides SNP locations and alleles for Homo
+sapiens extracted from NCBI dbSNP Build 144.  The source data files used for
+this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
+to reference genome GRCh37.p13.  Note that the GRCh37.p13 genome is a
+patched version of GRCh37.  However the patch doesn't alter chromosomes 1-22,
+X, Y, MT.  GRCh37 itself is the same as the hg19 genome from UCSC *except* for
+the mitochondrion chromosome.  Therefore, the SNPs in this package can be
+injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
+correct position but this injection will exclude chrM (i.e. nothing will be
+injected in that sequence).")
+    (license license:artistic2.0)))
+
 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
   (package
     (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
@@ -11271,44 +11309,6 @@ (define-public r-seqbias
 genome sequence.")
     (license license:lgpl3)))
 
-(define-public r-snplocs-hsapiens-dbsnp144-grch37
-  (package
-    (name "r-snplocs-hsapiens-dbsnp144-grch37")
-    (version "0.99.20")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
-                                     version 'annotation))
-              (sha256
-               (base32
-                "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
-    (build-system r-build-system)
-    ;; As this package provides little more than a very large data file it
-    ;; doesn't make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
-    (propagated-inputs
-     (list r-biocgenerics
-           r-s4vectors
-           r-iranges
-           r-genomeinfodb
-           r-genomicranges
-           r-bsgenome
-           r-biostrings))
-    (home-page
-     "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
-    (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
-    (description "This package provides SNP locations and alleles for Homo
-sapiens extracted from NCBI dbSNP Build 144.  The source data files used for
-this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
-to reference genome GRCh37.p13.  Note that the GRCh37.p13 genome is a
-patched version of GRCh37.  However the patch doesn't alter chromosomes 1-22,
-X, Y, MT.  GRCh37 itself is the same as the hg19 genome from UCSC *except* for
-the mitochondrion chromosome.  Therefore, the SNPs in this package can be
-injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
-correct position but this injection will exclude chrM (i.e. nothing will be
-injected in that sequence).")
-    (license license:artistic2.0)))
-
 (define-public r-reqon
   (package
     (name "r-reqon")
-- 
cgit v1.2.3


From 919cecd00b018d596cf8aca10b370c4d91989be9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 14 Apr 2022 13:38:30 +0200
Subject: gnu: r-illuminahumanmethylation450kanno-ilmn12-hg19: Move to
 annotation section.

* gnu/packages/bioconductor.scm (r-illuminahumanmethylation450kanno-ilmn12-hg19):
Move this variable up to the annotation section.
---
 gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++----------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 094bd0d907..2fa64c4b0b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -557,6 +557,32 @@ (define-public r-mus-musculus
 from several related annotation packages.")
     (license license:artistic2.0)))
 
+(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
+  (package
+    (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri
+             "IlluminaHumanMethylation450kanno.ilmn12.hg19"
+             version 'annotation))
+       (sha256
+        (base32
+         "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
+    (properties
+     `((upstream-name
+        . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-minfi))
+    (home-page
+     "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
+    (synopsis "Annotation for Illumina's 450k methylation arrays")
+    (description
+     "This package provides manifests and annotation for Illumina's 450k array
+data.")
+    (license license:artistic2.0)))
+
 (define-public r-org-ce-eg-db
   (package
     (name "r-org-ce-eg-db")
@@ -11134,32 +11160,6 @@ (define-public r-roc
 Characteristic} (ROC) curves, with a focus on micro arrays.")
     (license license:artistic2.0)))
 
-(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
-  (package
-    (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
-    (version "0.6.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri
-             "IlluminaHumanMethylation450kanno.ilmn12.hg19"
-             version 'annotation))
-       (sha256
-        (base32
-         "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
-    (properties
-     `((upstream-name
-        . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-minfi))
-    (home-page
-     "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
-    (synopsis "Annotation for Illumina's 450k methylation arrays")
-    (description
-     "This package provides manifests and annotation for Illumina's 450k array
-data.")
-    (license license:artistic2.0)))
-
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-- 
cgit v1.2.3


From b0dd06bd0caea46a852248ab48ab2e6aaff57752 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 11 Apr 2022 16:03:35 +0200
Subject: gnu: Add r-xcir.

* gnu/packages/bioconductor.scm (r-xcir): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 39 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2fa64c4b0b..bec3496057 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
@@ -5191,6 +5191,43 @@ (define-public r-vsn
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
+;; There is no source tarball, so we fetch the code from the Bioconductor git
+;; repository.
+(define-public r-xcir
+  (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
+        (revision "1"))
+    (package
+      (name "r-xcir")
+      (version (git-version "1.8.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.bioconductor.org/packages/XCIR")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
+      (properties `((upstream-name . "XCIR")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-biomart
+                               r-biostrings
+                               r-data-table
+                               r-ggplot2
+                               r-iranges
+                               r-readxl
+                               r-s4vectors
+                               r-seqminer
+                               r-variantannotation))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/SRenan/XCIR")
+      (synopsis "Analysis of X chromosome inactivation")
+      (description
+       "This package is an R package that offers models and tools for subject
+level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
+inference.")
+      (license license:gpl2))))
+
 (define-public r-xina
   (package
     (name "r-xina")
-- 
cgit v1.2.3


From 2902adfc7e0e4e9526ead9d35be14ac4f9b77c1c Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Sun, 17 Apr 2022 10:13:43 +0200
Subject: gnu: Add r-adam.

* gnu/packages/bioconductor.scm (r-adam): New variable.
---
 gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bec3496057..cd28d3eb20 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1581,6 +1581,41 @@ (define-public r-absseq
 ranking by fold-change and visualization.")
     (license license:gpl3+)))
 
+(define-public r-adam
+  (package
+    (name "r-adam")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ADAM" version))
+              (sha256
+               (base32
+                "18zwci0ab54q7rdwj0n63w0i14lfrb4cccp09bcrq10gl1ki07f5"))))
+    (properties `((upstream-name . "ADAM")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-dplyr
+                             r-dt
+                             r-go-db
+                             r-keggrest
+                             r-knitr
+                             r-pbapply
+                             r-rcpp
+                             r-stringr
+                             r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ADAM")
+    (synopsis "Gene activity and diversity analysis module")
+    (description
+     "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
+package created to group a set of genes from comparative samples (control
+versus experiment) belonging to different species according to their respective
+functions.  The corresponding roles are extracted from the default collections
+like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
+@code{ADAM} show their significance by calculating the p-values referring to
+gene diversity and activity.  Each group of genes is called @dfn{Group of
+functionally associated genes} (GFAG).")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From b79431b5e98d33c23dea808d0aa9fd847e1471ab Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 26 Apr 2022 09:45:43 +0200
Subject: gnu: Add r-lfa.

* gnu/packages/bioconductor.scm (r-lfa): New variable.
---
 gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cd28d3eb20..fa862d736f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3793,6 +3793,27 @@ (define-public r-keggrest
 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
     (license license:artistic2.0)))
 
+(define-public r-lfa
+  (package
+    (name "r-lfa")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "lfa" version))
+       (sha256
+        (base32 "02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr"))))
+    (properties `((upstream-name . "lfa")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-corpcor))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/StoreyLab/lfa")
+    (synopsis "Logistic Factor Analysis for categorical data")
+    (description
+     "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
+Binomial data via estimation of latent structure in the natural parameter.")
+    (license license:gpl3)))
+
 (define-public r-limma
   (package
     (name "r-limma")
-- 
cgit v1.2.3


From 936f23a654d4b1a29840792b1802d78e378275a5 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 26 Apr 2022 12:19:54 +0200
Subject: gnu: Add r-adamgui.

* gnu/packages/bioconductor.scm (r-adamgui): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fa862d736f..67ee6079c6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1616,6 +1616,54 @@ (define-public r-adam
 functionally associated genes} (GFAG).")
     (license license:gpl2+)))
 
+(define-public r-adamgui
+  (package
+    (name "r-adamgui")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ADAMgui" version))
+              (sha256
+               (base32
+                "0n06bb9djigha0249lxx84pn9q0xiryxbv25qsc3p2h46iaxi3wq"))))
+    (properties `((upstream-name . "ADAMgui")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-adam
+           r-colorramps
+           r-data-table
+           r-dplyr
+           r-dt
+           r-ggplot2
+           r-ggpubr
+           r-ggrepel
+           r-ggsignif
+           r-go-db
+           r-gridextra
+           r-knitr
+           r-rcolorbrewer
+           r-reshape2
+           r-shiny
+           r-shinyjs
+           r-stringi
+           r-stringr
+           r-testthat
+           r-varhandle))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ADAMgui/")
+    (synopsis "GUI for gene activity and diversity analysis")
+    (description
+     "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
+for the @code{ADAM} package.  The @code{ADAMgui} package provides two
+shiny-based applications that allows the user to study the output of the
+@code{ADAM} package files through different plots.  It's possible, for
+example, to choose a specific @dfn{group of functionally associated
+genes} (GFAG) and observe the gene expression behavior with the plots created
+with the @code{GFAGtargetUi} function.  Features such as differential
+expression and fold change can be easily seen with aid of the plots made with
+the @code{GFAGpathUi} function.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From a45dfa8a731c9ba2626ee7ca19e7d61f2e82925d Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 26 Apr 2022 13:36:23 +0200
Subject: gnu: Add r-adimpute.

* gnu/packages/bioconductor.scm (r-adimpute): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 67ee6079c6..f55416ef43 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1664,6 +1664,55 @@ (define-public r-adamgui
 the @code{GFAGpathUi} function.")
     (license license:gpl2+)))
 
+(define-public r-adimpute
+  (package
+    (name "r-adimpute")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "ADImpute" version))
+              (sha256
+               (base32
+                "1bkq1hd8sqg9r28r70a9vd3gb2nsmg6dybf002d621p88cdfjib2"))))
+    (properties `((upstream-name . "ADImpute")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-checkmate
+           r-data-table
+           r-drimpute
+           r-kernlab
+           r-mass
+           r-matrix
+           r-rsvd
+           r-s4vectors
+           r-saver
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/ADImpute")
+    (synopsis "Adaptive computational prediction for dropout imputations")
+    (description
+     "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
+unable to quantify the expression levels of all genes in a cell, creating a
+need for the computational prediction of missing values (dropout imputation).
+Most existing dropout imputation methods are limited in the sense that they
+exclusively use the scRNA-seq dataset at hand and do not exploit external
+gene-gene relationship information.  The @code{ADImpute} package proposes two
+methods to address this issue:
+
+@enumerate
+@item a gene regulatory network-based approach using gene-gene relationships
+  learnt from external data;
+@item a baseline approach corresponding to a sample-wide average.
+@end enumerate
+
+@code{ADImpute} implements these novel methods and also combines them with
+existing imputation methods like @code{DrImpute} and @code{SAVER}.
+@code{ADImpute} can learn the best performing method per gene and combine the
+results from different methods into an ensemble.")
+    (license license:gpl3+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From 43dc50a5c7271cbdea15b0e14ce69668191cfdaa Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 26 Apr 2022 16:07:09 +0200
Subject: gnu: Add r-adsplit.

* gnu/packages/bioconductor.scm (r-adsplit): New variable.
---
 gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f55416ef43..6b718b7e10 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1713,6 +1713,34 @@ (define-public r-adimpute
 results from different methods into an ensemble.")
     (license license:gpl3+)))
 
+(define-public r-adsplit
+  (package
+    (name "r-adsplit")
+    (version "1.64.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "adSplit" version))
+              (sha256
+               (base32
+                "1b4ck371h3a76m5h0brvlzsyg1g6q5fjrhra5hqv9pwxr330h9r2"))))
+    (properties `((upstream-name . "adSplit")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-annotationdbi
+           r-biobase
+           r-cluster
+           r-go-db
+           r-keggrest
+           r-multtest))
+    (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
+    (synopsis "Annotation-driven splits in microarray data")
+    (description
+     "This package implements clustering of microarray gene expression
+profiles according to functional annotations.  For each term genes are
+annotated to, splits into two subclasses are computed and a significance of
+the supporting gene set is determined.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From 851770312fc3aed467494112174205388c49afc2 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 26 Apr 2022 17:24:55 +0200
Subject: gnu: Add r-affixcan.

* gnu/packages/bioconductor.scm (r-affixcan): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6b718b7e10..bbbe649320 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1741,6 +1741,34 @@ (define-public r-adsplit
 the supporting gene set is determined.")
     (license license:gpl2+)))
 
+(define-public r-affixcan
+  (package
+    (name "r-affixcan")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AffiXcan" version))
+              (sha256
+               (base32
+                "06yn87briv2141jqad934gg5rcd90w5nghrgmbhqnmwafn72gj9d"))))
+    (properties `((upstream-name . "AffiXcan")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-crayon
+           r-multiassayexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AffiXcan")
+    (synopsis "Functional approach to impute genetically regulated expression")
+    (description
+     "The @code{AffiXcan} package imputes a @dfn{genetically regulated
+expression} (GReX) for a set of genes in a sample of individuals, using a
+method based on the @dfn{total binding affinity} (TBA).  Statistical models to
+impute GReX can be trained with a training dataset where the real total
+expression values are known.")
+    (license license:gpl3)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From be2ead307371ae03d0b56652fc40bec11869b8a1 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 27 Apr 2022 12:56:14 +0200
Subject: gnu: Add r-affyrnadegradation.

* gnu/packages/bioconductor.scm (r-affyrnadegradation): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bbbe649320..088d50f7f5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1769,6 +1769,31 @@ (define-public r-affixcan
 expression values are known.")
     (license license:gpl3)))
 
+(define-public r-affyrnadegradation
+  (package
+    (name "r-affyrnadegradation")
+    (version "1.40.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AffyRNADegradation" version))
+              (sha256
+               (base32
+                "00hzr62xn1i1w4g8krsxhivzwn8hd7hwhkdxyrpz6cs9vgr4x9kd"))))
+    (properties `((upstream-name . "AffyRNADegradation")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-affy))
+    (home-page "https://bioconductor.org/packages/AffyRNADegradation")
+    (synopsis
+     "Analyze and correct probe positional bias in data due to RNA degradation")
+    (description
+     "The @code{AffyRNADegradation} package helps with the assessment and
+correction of RNA degradation effects in Affymetrix 3 expression arrays.  The
+parameter @code{d} gives a robust and accurate measure of RNA integrity.  The
+correction removes the probe positional bias, and thus improves comparability
+of samples that are affected by RNA degradation.")
+    ;; the R file header specifies GPL2 or later
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From 73fe0dab503c3a2d2a2dac291e3d3809872acbf4 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 27 Apr 2022 13:20:14 +0200
Subject: gnu: Add r-agdex.

* gnu/packages/bioconductor.scm (r-agdex): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 088d50f7f5..3d68db6d68 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1794,6 +1794,33 @@ (define-public r-affyrnadegradation
     ;; the R file header specifies GPL2 or later
     (license license:gpl2+)))
 
+(define-public r-agdex
+  (package
+    (name "r-agdex")
+    (version "1.42.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AGDEX" version))
+              (sha256
+               (base32
+                "0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64"))))
+    (properties `((upstream-name . "AGDEX")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-gseabase))
+    (home-page "https://bioconductor.org/packages/AGDEX")
+    (synopsis
+     "Evaluate agreement of differential expression for cross-species genomics")
+    (description
+     "The objective of @code{AGDEX} is to evaluate whether the results of a
+pair of two-group differential expression analysis comparisons show a level of
+agreement that is greater than expected if the group labels for each two-group
+comparison are randomly assigned.  The agreement is evaluated for the entire
+transcriptome and (optionally) for a collection of pre-defined gene-sets.
+Additionally, the procedure performs permutation-based differential expression
+and meta analysis at both gene and gene-set levels of the data from each
+experiment.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From 37f584592ad7ac1ce9644b14bf96a2620be0b237 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 27 Apr 2022 13:44:36 +0200
Subject: gnu: Add r-aggregatebiovar.

* gnu/packages/bioconductor.scm (r-aggregatebiovar): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3d68db6d68..b760db2db7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1821,6 +1821,40 @@ (define-public r-agdex
 experiment.")
     (license license:gpl2+)))
 
+(define-public r-aggregatebiovar
+  (package
+    (name "r-aggregatebiovar")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "aggregateBioVar" version))
+              (sha256
+               (base32
+                "1wbfp1pf62di6pzxsf36lmzk6y9dllz1n4iv3mhpb1x8cvy4hqqk"))))
+    (properties `((upstream-name . "aggregateBioVar")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-matrix
+           r-rlang
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-tibble))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/jasonratcliff/aggregateBioVar")
+    (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
+    (description
+     "This package @code{aggregateBioVar} contains tools to summarize single
+cell gene expression profiles at the level of subject for single cell RNA-seq
+data collected from more than one subject (e.g. biological sample or technical
+replicates).  A @code{SingleCellExperiment} object is taken as input and
+converted to a list of @code{SummarizedExperiment} objects, where each list
+element corresponds to an assigned cell type.  The @code{SummarizedExperiment}
+objects contain aggregate gene-by-subject count matrices and inter-subject
+column metadata for individual subjects that can be processed using downstream
+bulk RNA-seq tools.")
+    (license license:gpl3)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From 31c9f0e30108bc9845df85e9b3f440d53b002409 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Wed, 27 Apr 2022 14:50:15 +0200
Subject: gnu: Add r-agilp.

* gnu/packages/bioconductor.scm (r-agilp): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b760db2db7..a78903becc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1855,6 +1855,28 @@ (define-public r-aggregatebiovar
 bulk RNA-seq tools.")
     (license license:gpl3)))
 
+(define-public r-agilp
+  (package
+    (name "r-agilp")
+    (version "3.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "agilp" version))
+              (sha256
+               (base32
+                "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp"))))
+    (properties `((upstream-name . "agilp")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/agilp")
+    (synopsis "Processing of Agilent expression array")
+    (description
+     "This package aims to provide a pipeline for the low-level analysis of
+gene expression microarray data, primarily focused on the Agilent platform,
+but which also provides utilities which may be useful for other platforms.")
+    ;; Some files are under GPLv2+ but the combined work is released under the
+    ;; GPLv3.
+    (license license:gpl3)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From 290934c8fccfb270ddaf5d8c1ca0a746ebd0e332 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Sun, 17 Apr 2022 17:10:44 +0200
Subject: gnu: Add r-adductdata.

* gnu/packages/bioconductor.scm (r-adductdata): New variable.
---
 gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a78903becc..f0462a5368 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1166,6 +1166,28 @@ (define-public r-abadata
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
+(define-public r-adductdata
+  (package
+    (name "r-adductdata")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "adductData" version 'experiment))
+              (sha256
+               (base32
+                "0bp74p06gskwn2xl1srpnmsq27ajsrlynkzw6fcmvwwjcrzljmnj"))))
+    (properties `((upstream-name . "adductData")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationhub r-experimenthub))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/adductData")
+    (synopsis "Data from untargeted mass spectrometry of modifications to Cys34")
+    (description
+     "This package contains data from untargeted @dfn{mass spectrometry} (MS)
+of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
+albumin} (HSA).")
+    (license license:artistic2.0)))
+
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")
-- 
cgit v1.2.3


From 9c19db8c1d848412697b0b47ff6e878248de1944 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Sun, 17 Apr 2022 17:10:46 +0200
Subject: gnu: Add r-adductomicsr.

* gnu/packages/bioconductor.scm (r-adductomicsr): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f0462a5368..2db0ab3752 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1899,6 +1899,51 @@ (define-public r-agilp
     ;; GPLv3.
     (license license:gpl3)))
 
+(define-public r-adductomicsr
+  (package
+    (name "r-adductomicsr")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "adductomicsR" version))
+              (sha256
+               (base32
+                "0cnvxrk0h3r6jpa4g4qismg6zk5c7rf8lqixg89c24i98gffkbcl"))))
+    (properties `((upstream-name . "adductomicsR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-adductdata
+           r-ade4
+           r-annotationhub
+           r-bootstrap
+           r-data-table
+           r-dosnow
+           r-dplyr
+           r-dt
+           r-experimenthub
+           r-fastcluster
+           r-foreach
+           r-fpc
+           r-mzr
+           r-orgmassspecr
+           r-pastecs
+           r-pracma
+           r-rcppeigen
+           r-reshape2
+           r-rvest
+           r-smoother
+           r-zoo))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/adductomicsR")
+    (synopsis "Processing of adductomic mass spectral datasets")
+    (description
+     "This package @code{adductomicsR} processes data generated by the
+@dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
+peptides from spectra that has been corrected for mass drift and retention
+time drift and quantifies level mass spectral peaks from @dfn{first stage of
+mass spectrometry} (MS1) data.")
+    (license license:artistic2.0)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From 7494f4b4ab94504ac1c8ac71d53ab6ab9c552da1 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 2 May 2022 11:37:34 +0200
Subject: gnu: Add r-agimicrorna.

* gnu/packages/bioconductor.scm (r-agimicrorna): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2db0ab3752..80cf28c954 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1944,6 +1944,36 @@ (define-public r-adductomicsr
 mass spectrometry} (MS1) data.")
     (license license:artistic2.0)))
 
+(define-public r-agimicrorna
+  (package
+    (name "r-agimicrorna")
+    (version "2.46.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AgiMicroRna" version))
+              (sha256
+               (base32
+                "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
+    (properties `((upstream-name . "AgiMicroRna")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affy
+           r-affycoretools
+           r-biobase
+           r-limma
+           r-preprocesscore))
+    (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
+    (synopsis
+     "Processing and differential expression analysis of Agilent microRNA chips")
+    (description
+     "@code{AgiMicroRna} provides useful functionality for the processing,
+quality assessment and differential expression analysis of Agilent microRNA
+array data.  The package uses a limma-like structure to generate the processed
+data in order to make statistical inferences about differential expression
+using the linear model features implemented in limma.  Standard Bioconductor
+objects are used so that other packages could be used as well.")
+    (license license:gpl3)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
cgit v1.2.3


From caa51b5d1032e31f674a7ccd1bf0a6408a5825ff Mon Sep 17 00:00:00 2001
From: zimoun <zimon.toutoune@gmail.com>
Date: Tue, 24 May 2022 20:08:50 +0200
Subject: gnu: Add r-pscbs.

* gnu/packages/bioconductor.scm (r-pscbs): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 80cf28c954..4baa80dcb1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4560,6 +4560,48 @@ (define-public r-pcamethods
 structure (pcaRes) to provide a common interface to the PCA results.")
     (license license:gpl3+)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package:
+;; r-aroma-light, r-dnacopy..
+(define-public r-pscbs
+  (package
+    (name "r-pscbs")
+    (version "0.66.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "PSCBS" version))
+       (sha256
+        (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
+    (properties `((upstream-name . "PSCBS")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-aroma-light
+           r-dnacopy
+           r-future
+           r-listenv
+           r-matrixstats
+           r-r-cache
+           r-r-methodss3
+           r-r-oo
+           r-r-utils))
+    (native-inputs
+     (list r-r-rsp                      ;used to build vignettes
+           r-r-devices))
+    (home-page "https://github.com/HenrikBengtsson/PSCBS")
+    (synopsis "Analysis of parent-specific DNA copy numbers")
+    (description
+     "This is a package for segmentation of allele-specific DNA copy number
+data and detection of regions with abnormal copy number within each parental
+chromosome.  Both tumor-normal paired and tumor-only analyses are supported.")
+    (license license:gpl2+)))
+
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-- 
cgit v1.2.3


From ac12a57b7836dfbb8539fb27f570632c94c7cc12 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 08:30:02 +0200
Subject: gnu: r-activepathways: Update to 1.1.0.

* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.1.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4baa80dcb1..7c7bf84aea 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12317,14 +12317,14 @@ (define-public r-activedriverwgs
 (define-public r-activepathways
   (package
     (name "r-activepathways")
-    (version "1.0.4")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActivePathways" version))
        (sha256
         (base32
-         "1prhwx0nnwy2q62l2r0z31mhk4mq6xdr6mjihdlwpwgwq4rfi60y"))))
+         "0zbrgz91mlik7j8j11wsdswqqqfsijj8jkgd5fx1ar3mc6rqsmbg"))))
     (properties
      `((upstream-name . "ActivePathways")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3ceaa41e67b20cfb0f2a1ec772fe01bbb1651c53 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 08:30:08 +0200
Subject: gnu: r-wgcna: Update to 1.71.

* gnu/packages/bioconductor.scm (r-wgcna): Update to 1.71.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c7bf84aea..ba6a015595 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13567,14 +13567,14 @@ (define-public r-s4vectors
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.70-3")
+    (version "1.71")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
+         "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3360f14b080e6718785c73844abfc02c40f6a965 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 08:30:08 +0200
Subject: gnu: r-ldheatmap: Update to 1.0-6.

* gnu/packages/bioconductor.scm (r-ldheatmap): Update to 1.0-6.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ba6a015595..87f8543cf2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14832,14 +14832,14 @@ (define-public r-ldblock
 (define-public r-ldheatmap
   (package
     (name "r-ldheatmap")
-    (version "1.0-4")
+    (version "1.0-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "LDheatmap" version))
        (sha256
         (base32
-         "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
+         "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
     (properties `((upstream-name . "LDheatmap")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 32a3b09c51a8c3f4075dbf1215b7b5efa3f3ea2a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 08:30:09 +0200
Subject: gnu: r-abn: Update to 2.7-1.

* gnu/packages/bioconductor.scm (r-abn): Update to 2.7-1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 87f8543cf2..bf371a970a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14858,14 +14858,14 @@ (define-public r-ldheatmap
 (define-public r-abn
   (package
     (name "r-abn")
-    (version "2.7-0")
+    (version "2.7-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abn" version))
        (sha256
         (base32
-         "13i2f4lw1rzj89bp31sn03prq1bqj7bsxwdr8z2ql02yqks9phg0"))))
+         "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
     (build-system r-build-system)
     (inputs
      (list gsl))
-- 
cgit v1.2.3


From d723619fc30667514fea944256bd55afe5e219f0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 10:34:30 +0200
Subject: gnu: r-biostrings: Patch for R 4.2.0.

* gnu/packages/bioconductor.scm (r-biostrings)[arguments]: Add build phase
'patch-for-R-4.2.0.
---
 gnu/packages/bioconductor.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bf371a970a..0410ff8a82 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3104,6 +3104,19 @@ (define-public r-biostrings
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         ;; See commit c3340745870a88d1558e093a7f892c1aeac784ef in
+         ;; https://github.com/Bioconductor/Biostrings/
+         (add-after 'unpack 'patch-for-R-4.2.0
+           (lambda _
+             (substitute* '("src/BitMatrix.c"
+                            "src/RoSeqs_utils.c"
+                            "src/match_pdict_utils.c"
+                            "src/xscat.c")
+               (("#include <S.h>.*")
+                "#define Salloc(n,t) (t*)S_alloc(n, sizeof(t))  /* from old <S.h> */\n")))))))
     (propagated-inputs
      (list r-biocgenerics
            r-crayon
-- 
cgit v1.2.3


From 413133e4309a19c4830170271ee58c6cd9f0ff62 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:19:36 +0200
Subject: gnu: Add r-decoupler.

* gnu/packages/bioconductor.scm (r-decoupler): New variable.
---
 gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0410ff8a82..4e06a3c694 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2167,6 +2167,47 @@ (define-public r-decipher
 biological sequences.")
     (license license:gpl3)))
 
+(define-public r-decoupler
+  (package
+    (name "r-decoupler")
+    (version "2.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "decoupleR" version))
+       (sha256
+        (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
+    (properties `((upstream-name . "decoupleR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-broom
+           r-dplyr
+           r-magrittr
+           r-matrix
+           r-purrr
+           r-rlang
+           r-stringr
+           r-tibble
+           r-tidyr
+           r-tidyselect
+           r-withr))
+    (native-inputs (list r-knitr))
+    (home-page "https://saezlab.github.io/decoupleR/")
+    (synopsis "Computational methods to infer biological activities from omics data")
+    (description
+     "Many methods allow us to extract biological activities from omics data using
+information from prior knowledge resources, reducing the dimensionality for
+increased statistical power and better interpretability.  decoupleR is a
+Bioconductor package containing different statistical methods to extract these
+signatures within a unified framework.  decoupleR allows the user to flexibly
+test any method with any resource.  It incorporates methods that take into
+account the sign and weight of network interactions.  decoupleR can be used
+with any omic, as long as its features can be linked to a biological process
+based on prior knowledge.  For example, in transcriptomics gene sets regulated
+by a transcription factor, or in phospho-proteomics phosphosites that are
+targeted by a kinase.")
+    (license license:gpl3)))
+
 (define-public r-deepsnv
   (package
     (name "r-deepsnv")
-- 
cgit v1.2.3


From 90d165ea864439744772575c1b8d469576d1f419 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:23:09 +0200
Subject: gnu: r-biostrings: Update to 2.64.0.

* gnu/packages/bioconductor.scm (r-biostrings): Update to 2.64.0.
[arguments]: Remove build phase 'patch-for-R-4.2.0.
---
 gnu/packages/bioconductor.scm | 17 ++---------------
 1 file changed, 2 insertions(+), 15 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4e06a3c694..0635890a4f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3135,29 +3135,16 @@ (define-public r-biocparallel
 (define-public r-biostrings
   (package
     (name "r-biostrings")
-    (version "2.62.0")
+    (version "2.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biostrings" version))
               (sha256
                (base32
-                "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq"))))
+                "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8"))))
     (properties
      `((upstream-name . "Biostrings")))
     (build-system r-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         ;; See commit c3340745870a88d1558e093a7f892c1aeac784ef in
-         ;; https://github.com/Bioconductor/Biostrings/
-         (add-after 'unpack 'patch-for-R-4.2.0
-           (lambda _
-             (substitute* '("src/BitMatrix.c"
-                            "src/RoSeqs_utils.c"
-                            "src/match_pdict_utils.c"
-                            "src/xscat.c")
-               (("#include <S.h>.*")
-                "#define Salloc(n,t) (t*)S_alloc(n, sizeof(t))  /* from old <S.h> */\n")))))))
     (propagated-inputs
      (list r-biocgenerics
            r-crayon
-- 
cgit v1.2.3


From 67d858b97cc6dc7a10ca38b1e6390192ff3bf765 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:36:49 +0200
Subject: gnu: r-abarray: Update to 1.64.0.

* gnu/packages/bioconductor.scm (r-abarray): Update to 1.64.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0635890a4f..a426d825de 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1551,13 +1551,13 @@ (define-public r-tcgabiolinksgui-data
 (define-public r-abarray
   (package
     (name "r-abarray")
-    (version "1.62.0")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABarray" version))
               (sha256
                (base32
-                "0yh7jmkwdg3kmm98ii0cxbla3s5bwy84fpg6xcpggsrriwzwfb5k"))))
+                "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
     (properties `((upstream-name . "ABarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-multtest))
-- 
cgit v1.2.3


From 5911a8992bf149363ba518ea6911aae8ddb3b417 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:30 +0200
Subject: gnu: r-absseq: Update to 1.50.0.

* gnu/packages/bioconductor.scm (r-absseq): Update to 1.50.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a426d825de..1b40b2f528 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1577,13 +1577,13 @@ (define-public r-abarray
 (define-public r-absseq
   (package
     (name "r-absseq")
-    (version "1.48.0")
+    (version "1.50.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ABSSeq" version))
               (sha256
                (base32
-                "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650"))))
+                "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
     (properties `((upstream-name . "ABSSeq")))
     (build-system r-build-system)
     (propagated-inputs (list r-limma r-locfit))
-- 
cgit v1.2.3


From 69dc67d9aa41a9310c01abaa575b4edfc2e50f98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:30 +0200
Subject: gnu: r-adam: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-adam): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1b40b2f528..494a164f0e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1606,13 +1606,13 @@ (define-public r-absseq
 (define-public r-adam
   (package
     (name "r-adam")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAM" version))
               (sha256
                (base32
-                "18zwci0ab54q7rdwj0n63w0i14lfrb4cccp09bcrq10gl1ki07f5"))))
+                "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
     (properties `((upstream-name . "ADAM")))
     (build-system r-build-system)
     (propagated-inputs (list r-dplyr
-- 
cgit v1.2.3


From 1d3b5f80e75375fc91db4ae0c9ae0d2ac171a7e5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:30 +0200
Subject: gnu: r-adamgui: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 494a164f0e..09604239eb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1641,13 +1641,13 @@ (define-public r-adam
 (define-public r-adamgui
   (package
     (name "r-adamgui")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADAMgui" version))
               (sha256
                (base32
-                "0n06bb9djigha0249lxx84pn9q0xiryxbv25qsc3p2h46iaxi3wq"))))
+                "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
     (properties `((upstream-name . "ADAMgui")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3a29b78fa9161473aff8d076cde247870cea05e9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:30 +0200
Subject: gnu: r-adimpute: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-adimpute): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 09604239eb..27216b2b52 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1689,13 +1689,13 @@ (define-public r-adamgui
 (define-public r-adimpute
   (package
     (name "r-adimpute")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ADImpute" version))
               (sha256
                (base32
-                "1bkq1hd8sqg9r28r70a9vd3gb2nsmg6dybf002d621p88cdfjib2"))))
+                "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
     (properties `((upstream-name . "ADImpute")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3e524e46a043711db22c17352156294e40d7321c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:30 +0200
Subject: gnu: r-adsplit: Update to 1.66.0.

* gnu/packages/bioconductor.scm (r-adsplit): Update to 1.66.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 27216b2b52..4e2ff9ebd6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1738,13 +1738,13 @@ (define-public r-adimpute
 (define-public r-adsplit
   (package
     (name "r-adsplit")
-    (version "1.64.0")
+    (version "1.66.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adSplit" version))
               (sha256
                (base32
-                "1b4ck371h3a76m5h0brvlzsyg1g6q5fjrhra5hqv9pwxr330h9r2"))))
+                "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
     (properties `((upstream-name . "adSplit")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From f4a85d5555c40bdeccb1894fbda5fcd2e2f97a4b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:30 +0200
Subject: gnu: r-affixcan: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-affixcan): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4e2ff9ebd6..b0a4731ae7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1766,13 +1766,13 @@ (define-public r-adsplit
 (define-public r-affixcan
   (package
     (name "r-affixcan")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffiXcan" version))
               (sha256
                (base32
-                "06yn87briv2141jqad934gg5rcd90w5nghrgmbhqnmwafn72gj9d"))))
+                "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
     (properties `((upstream-name . "AffiXcan")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 052d0d283adb58c12854bd5fa2259a2f64b89516 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:31 +0200
Subject: gnu: r-affyrnadegradation: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-affyrnadegradation): Update to 1.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b0a4731ae7..b4edb6e3c7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1794,13 +1794,13 @@ (define-public r-affixcan
 (define-public r-affyrnadegradation
   (package
     (name "r-affyrnadegradation")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AffyRNADegradation" version))
               (sha256
                (base32
-                "00hzr62xn1i1w4g8krsxhivzwn8hd7hwhkdxyrpz6cs9vgr4x9kd"))))
+                "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
     (properties `((upstream-name . "AffyRNADegradation")))
     (build-system r-build-system)
     (propagated-inputs (list r-affy))
-- 
cgit v1.2.3


From 6e1d25615130944cdc14fe9498b49aa2ccce069b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:31 +0200
Subject: gnu: r-agdex: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-agdex): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b4edb6e3c7..137886f8f4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1819,13 +1819,13 @@ (define-public r-affyrnadegradation
 (define-public r-agdex
   (package
     (name "r-agdex")
-    (version "1.42.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AGDEX" version))
               (sha256
                (base32
-                "0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64"))))
+                "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
     (properties `((upstream-name . "AGDEX")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-gseabase))
-- 
cgit v1.2.3


From e704ed78b5f34c52afbb7e1a6d3fd3b49eeb66ac Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:31 +0200
Subject: gnu: r-aggregatebiovar: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-aggregatebiovar): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 137886f8f4..2f8cad9128 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1846,13 +1846,13 @@ (define-public r-agdex
 (define-public r-aggregatebiovar
   (package
     (name "r-aggregatebiovar")
-    (version "1.4.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aggregateBioVar" version))
               (sha256
                (base32
-                "1wbfp1pf62di6pzxsf36lmzk6y9dllz1n4iv3mhpb1x8cvy4hqqk"))))
+                "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
     (properties `((upstream-name . "aggregateBioVar")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a5e1a37cdfdb88210b751866fcd317a4b792258f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:31 +0200
Subject: gnu: r-agilp: Update to 3.28.0.

* gnu/packages/bioconductor.scm (r-agilp): Update to 3.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2f8cad9128..64f12d1e05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1880,13 +1880,13 @@ (define-public r-aggregatebiovar
 (define-public r-agilp
   (package
     (name "r-agilp")
-    (version "3.26.0")
+    (version "3.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "agilp" version))
               (sha256
                (base32
-                "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp"))))
+                "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
     (properties `((upstream-name . "agilp")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/agilp")
-- 
cgit v1.2.3


From 5f9a73d6652f6c4c2ac50113a2cdf1f1091635bf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:31 +0200
Subject: gnu: r-adductomicsr: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-adductomicsr): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 64f12d1e05..294a2d96d0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1902,13 +1902,13 @@ (define-public r-agilp
 (define-public r-adductomicsr
   (package
     (name "r-adductomicsr")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adductomicsR" version))
               (sha256
                (base32
-                "0cnvxrk0h3r6jpa4g4qismg6zk5c7rf8lqixg89c24i98gffkbcl"))))
+                "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
     (properties `((upstream-name . "adductomicsR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 75628fc7ce22890344e582b6fd7a648548acb3dd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:31 +0200
Subject: gnu: r-aneufinder: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 294a2d96d0..c0a3858559 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1977,13 +1977,13 @@ (define-public r-agimicrorna
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AneuFinder" version))
               (sha256
                (base32
-                "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0"))))
+                "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From b19400063ef4f3b6f8533a1eab49a3bbc3992cbe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:31 +0200
Subject: gnu: r-biocversion: Update to 3.15.2.

* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.15.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c0a3858559..7754e5bce9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2019,14 +2019,14 @@ (define-public r-aneufinder
 (define-public r-biocversion
   (package
     (name "r-biocversion")
-    (version "3.14.0")
+    (version "3.15.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocVersion" version))
        (sha256
         (base32
-         "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik"))))
+         "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
     (properties `((upstream-name . "BiocVersion")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BiocVersion/")
-- 
cgit v1.2.3


From 00d51727e5d7ba89de5ad49a79f235e81130bff9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:32 +0200
Subject: gnu: r-biocgenerics: Update to 0.42.0.

* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7754e5bce9..dec8c299e4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2039,13 +2039,13 @@ (define-public r-biocversion
 (define-public r-biocgenerics
   (package
     (name "r-biocgenerics")
-    (version "0.40.0")
+    (version "0.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocGenerics" version))
               (sha256
                (base32
-                "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh"))))
+                "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
     (properties
      `((upstream-name . "BiocGenerics")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 6f0430cdc2a4fd2cb2e0b12984fb7877fd6d6a2f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:32 +0200
Subject: gnu: r-coverageview: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dec8c299e4..860417862a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2059,13 +2059,13 @@ (define-public r-biocgenerics
 (define-public r-coverageview
   (package
     (name "r-coverageview")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "CoverageView" version))
               (sha256
                (base32
-                "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as"))))
+                "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-s4vectors
-- 
cgit v1.2.3


From b0bd7ec471aed0c99e57a80666ee19a8b1cd0b36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:32 +0200
Subject: gnu: r-cummerbund: Update to 2.38.0.

* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 860417862a..aa0f4d4fb5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2086,13 +2086,13 @@ (define-public r-coverageview
 (define-public r-cummerbund
   (package
    (name "r-cummerbund")
-   (version "2.36.0")
+   (version "2.38.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "cummeRbund" version))
              (sha256
               (base32
-               "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql"))))
+               "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
-- 
cgit v1.2.3


From 25847e60fe22f2f82c62d2856b83f6ce882b329d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:32 +0200
Subject: gnu: r-dearseq: Update to 1.8.1.

* gnu/packages/bioconductor.scm (r-dearseq): Update to 1.8.1.
[propagated-inputs]: Add r-compquadform, r-dplyr, r-magrittr, r-reshape2, r-rlang,
r-tibble, and r-viridislite.
[native-inputs]: Add r-knitr.
---
 gnu/packages/bioconductor.scm | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aa0f4d4fb5..60c2177a6d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2116,24 +2116,32 @@ (define-public r-cummerbund
 (define-public r-dearseq
   (package
     (name "r-dearseq")
-    (version "1.6.0")
+    (version "1.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dearseq" version))
        (sha256
         (base32
-         "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc"))))
+         "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1"))))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ggplot2
+     (list r-compquadform
+           r-dplyr
+           r-ggplot2
            r-kernsmooth
+           r-magrittr
            r-matrixstats
            r-patchwork
            r-pbapply
+           r-reshape2
+           r-rlang
            r-statmod
            r-survey
-           r-kernsmooth))
+           r-tibble
+           r-viridislite))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://github.com/borishejblum/dearseq")
     (synopsis "DEA for RNA-seq data through a robust variance component test")
     (description
-- 
cgit v1.2.3


From 7149e667c1668274629d7fce9ec34ba58fa25149 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:32 +0200
Subject: gnu: r-decipher: Update to 2.24.0.

* gnu/packages/bioconductor.scm (r-decipher): Update to 2.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 60c2177a6d..aa3ecdb7f7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2154,13 +2154,13 @@ (define-public r-dearseq
 (define-public r-decipher
   (package
     (name "r-decipher")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DECIPHER" version))
               (sha256
                (base32
-                "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm"))))
+                "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
-- 
cgit v1.2.3


From d15f46c5cf381bc79cd3dcb96c879892b3c6c99d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:32 +0200
Subject: gnu: r-deepsnv: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aa3ecdb7f7..d5dc61ed33 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2219,13 +2219,13 @@ (define-public r-decoupler
 (define-public r-deepsnv
   (package
     (name "r-deepsnv")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "deepSNV" version))
               (sha256
                (base32
-                "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w"))))
+                "0si1x2bi5pff1dicpqg7hv4ziq46vm7lic72724ljsclpz9bfv6q"))))
     (properties `((upstream-name . "deepSNV")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a2173119ecb14f789f0681175d556a468aabdabc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:33 +0200
Subject: gnu: r-delayedarray: Update to 0.22.0.

* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d5dc61ed33..2dc17f2451 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2255,13 +2255,13 @@ (define-public r-deepsnv
 (define-public r-delayedarray
   (package
     (name "r-delayedarray")
-    (version "0.20.0")
+    (version "0.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "DelayedArray" version))
               (sha256
                (base32
-                "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj"))))
+                "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
     (properties
      `((upstream-name . "DelayedArray")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From cea1b9029a13d7fba12fc8bd7e201133f598d607 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:33 +0200
Subject: gnu: r-derfinderhelper: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-derfinderhelper): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2dc17f2451..335e2a7d4d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2285,13 +2285,13 @@ (define-public r-delayedarray
 (define-public r-derfinderhelper
   (package
     (name "r-derfinderhelper")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "derfinderHelper" version))
        (sha256
-        (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35"))))
+        (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
     (properties `((upstream-name . "derfinderHelper")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 59fff0e2d25346966cc7cfbf8ab16db83ad9df56 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:33 +0200
Subject: gnu: r-drimseq: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-drimseq): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 335e2a7d4d..dc9bd9e754 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2310,13 +2310,13 @@ (define-public r-derfinderhelper
 (define-public r-drimseq
   (package
     (name "r-drimseq")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DRIMSeq" version))
        (sha256
-        (base32 "0y2jb0hb633id038zmwnfny6h4ai77fdyy02f77vha1z8xg5nl02"))))
+        (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
     (properties `((upstream-name . "DRIMSeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 051b7e63f2ff9a7f9eaa93b47c84f029e1afffa7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:33 +0200
Subject: gnu: r-bluster: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-bluster): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dc9bd9e754..180277883e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2345,13 +2345,13 @@ (define-public r-drimseq
 (define-public r-bluster
   (package
    (name "r-bluster")
-   (version "1.4.0")
+   (version "1.6.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "bluster" version))
             (sha256
              (base32
-              "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm"))))
+              "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
    (properties `((upstream-name . "bluster")))
    (build-system r-build-system)
    (propagated-inputs
-- 
cgit v1.2.3


From 48c3389314d17a08c9da0db897e3ddd3c5bbe165 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:33 +0200
Subject: gnu: r-ideoviz: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-ideoviz): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 180277883e..f3cf34ffa4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2375,13 +2375,13 @@ (define-public r-bluster
 (define-public r-ideoviz
   (package
     (name "r-ideoviz")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IdeoViz" version))
               (sha256
                (base32
-                "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g"))))
+                "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
-- 
cgit v1.2.3


From 285b5cb7fa3e30ce6afc14c0b3736c48087d30d8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:33 +0200
Subject: gnu: r-iranges: Update to 2.30.0.

* gnu/packages/bioconductor.scm (r-iranges): Update to 2.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f3cf34ffa4..9f067d6985 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2399,13 +2399,13 @@ (define-public r-ideoviz
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.28.0")
+    (version "2.30.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg"))))
+                "0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From a15c457c59e49d6630fce53e5fa2004be0722fef Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:33 +0200
Subject: gnu: r-isoformswitchanalyzer: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-isoformswitchanalyzer): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f067d6985..710ab6625d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2427,13 +2427,13 @@ (define-public r-iranges
 (define-public r-isoformswitchanalyzer
   (package
     (name "r-isoformswitchanalyzer")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
        (sha256
-        (base32 "14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf"))))
+        (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
     (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 429e687e69ade4c1d606c7350b9437081ee34d46 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:34 +0200
Subject: gnu: r-affy: Update to 1.74.0.

* gnu/packages/bioconductor.scm (r-affy): Update to 1.74.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 710ab6625d..fb34ab4b52 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2629,14 +2629,14 @@ (define-public r-nmf
 (define-public r-affy
   (package
     (name "r-affy")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affy" version))
        (sha256
         (base32
-         "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a"))))
+         "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affyio
-- 
cgit v1.2.3


From 45a6d9c0f455705cea154c7135d13074dd418c4e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:34 +0200
Subject: gnu: r-affycomp: Update to 1.72.0.

* gnu/packages/bioconductor.scm (r-affycomp): Update to 1.72.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fb34ab4b52..03a2016ab4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2657,14 +2657,14 @@ (define-public r-affy
 (define-public r-affycomp
   (package
     (name "r-affycomp")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycomp" version))
        (sha256
         (base32
-         "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21"))))
+         "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
     (properties `((upstream-name . "affycomp")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase))
-- 
cgit v1.2.3


From 83f8f3ae081a4fb24046d52b186031d343c47315 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:34 +0200
Subject: gnu: r-affycompatible: Update to 1.56.0.

* gnu/packages/bioconductor.scm (r-affycompatible): Update to 1.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 03a2016ab4..7199083072 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2678,14 +2678,14 @@ (define-public r-affycomp
 (define-public r-affycompatible
   (package
     (name "r-affycompatible")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AffyCompatible" version))
        (sha256
         (base32
-         "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg"))))
+         "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
     (properties
      `((upstream-name . "AffyCompatible")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From d4af958ae8946054c830de4d5b27056eb3371a6c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:34 +0200
Subject: gnu: r-affycontam: Update to 1.54.0.

* gnu/packages/bioconductor.scm (r-affycontam): Update to 1.54.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7199083072..4ed2006699 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2704,14 +2704,14 @@ (define-public r-affycompatible
 (define-public r-affycontam
   (package
     (name "r-affycontam")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyContam" version))
        (sha256
         (base32
-         "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f"))))
+         "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
     (properties `((upstream-name . "affyContam")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From fb1fb2b8c234c80e3ba4aeab7a3b0b963d8967e4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:34 +0200
Subject: gnu: r-affycoretools: Update to 1.68.1.

* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.68.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4ed2006699..dd438d9934 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2727,14 +2727,14 @@ (define-public r-affycontam
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
-    (version "1.66.0")
+    (version "1.68.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
-         "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40"))))
+         "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From da1e879b9bfb939161949dadca9a3fd0c525a66f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:34 +0200
Subject: gnu: r-affyio: Update to 1.66.0.

* gnu/packages/bioconductor.scm (r-affyio): Update to 1.66.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dd438d9934..d8ed5ac0d5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2769,14 +2769,14 @@ (define-public r-affycoretools
 (define-public r-affyio
   (package
     (name "r-affyio")
-    (version "1.64.0")
+    (version "1.66.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affyio" version))
        (sha256
         (base32
-         "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm"))))
+         "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-zlibbioc))
-- 
cgit v1.2.3


From b928f25f51c16c9a9055452db8509ca0afe23b19 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:34 +0200
Subject: gnu: r-affxparser: Update to 1.68.1.

* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.68.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d8ed5ac0d5..9591a8237f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2793,14 +2793,14 @@ (define-public r-affyio
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.66.0")
+    (version "1.68.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal"))))
+         "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
-- 
cgit v1.2.3


From 2563aeb416a5027dcfb9083e4cb57bdd741d3853 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:35 +0200
Subject: gnu: r-annotate: Update to 1.74.0.

* gnu/packages/bioconductor.scm (r-annotate): Update to 1.74.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9591a8237f..7054499094 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2821,14 +2821,14 @@ (define-public r-affxparser
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84"))))
+         "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From 0dcb2df4e1d306a084964141fddb1c7598deab98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:35 +0200
Subject: gnu: r-annotationdbi: Update to 1.58.0.

* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.58.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7054499094..7852ae9a71 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2848,13 +2848,13 @@ (define-public r-annotate
 (define-public r-annotationdbi
   (package
     (name "r-annotationdbi")
-    (version "1.56.2")
+    (version "1.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationDbi" version))
               (sha256
                (base32
-                "01zwq14msbbwzxv8rgpmyr74ymvhq0vnmxkxxwd886iac5vjlgi8"))))
+                "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
     (properties
      `((upstream-name . "AnnotationDbi")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3db379730549a5e3958d522e3f88df0e4384c39f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:35 +0200
Subject: gnu: r-annotationfilter: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-annotationfilter): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7852ae9a71..b79b1bd13b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2878,13 +2878,13 @@ (define-public r-annotationdbi
 (define-public r-annotationfilter
   (package
     (name "r-annotationfilter")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "AnnotationFilter" version))
               (sha256
                (base32
-                "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w"))))
+                "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
     (properties
      `((upstream-name . "AnnotationFilter")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 282985f6c3636c386c06d74dca4f661710fbf183 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:35 +0200
Subject: gnu: r-annotationforge: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b79b1bd13b..2c02d09697 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2903,14 +2903,14 @@ (define-public r-annotationfilter
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz"))))
+         "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 0b2579cbe07482049da1a0ae55a295f92ffd86a5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:35 +0200
Subject: gnu: r-annotationhub: Update to 3.4.0.

* gnu/packages/bioconductor.scm (r-annotationhub): Update to 3.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2c02d09697..e68f49fff1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2935,14 +2935,14 @@ (define-public r-annotationforge
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-    (version "3.2.2")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationHub" version))
        (sha256
         (base32
-         "08dk4h07gpi3rk9s80wrbx2ww2chj688qzbwlx8n4dz788lqbfz8"))))
+         "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
     (properties `((upstream-name . "AnnotationHub")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 043b388f387bcaaa488e77b4e915f04249d93635 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:35 +0200
Subject: gnu: r-aroma-light: Update to 3.26.0.

* gnu/packages/bioconductor.scm (r-aroma-light): Update to 3.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e68f49fff1..765e81efca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2976,14 +2976,14 @@ (define-public r-annotationhub
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-    (version "3.24.0")
+    (version "3.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "aroma.light" version))
        (sha256
         (base32
-         "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp"))))
+         "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
     (properties `((upstream-name . "aroma.light")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4d9011c00bd17714609a6ad11448d9099e1b9f94 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:36 +0200
Subject: gnu: r-bamsignals: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-bamsignals): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 765e81efca..db3019463b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3000,14 +3000,14 @@ (define-public r-aroma-light
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bamsignals" version))
        (sha256
         (base32
-         "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"))))
+         "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
-- 
cgit v1.2.3


From 70b29256f650742393d80ce8f8f6778f5ad9950c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:36 +0200
Subject: gnu: r-biobase: Update to 2.56.0.

* gnu/packages/bioconductor.scm (r-biobase): Update to 2.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index db3019463b..aa3438067c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3030,13 +3030,13 @@ (define-public r-bamsignals
 (define-public r-biobase
   (package
     (name "r-biobase")
-    (version "2.54.0")
+    (version "2.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Biobase" version))
               (sha256
                (base32
-                "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww"))))
+                "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
     (properties
      `((upstream-name . "Biobase")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 48ca8c80267d3610c0d5367fa48b57122aba8acc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:36 +0200
Subject: gnu: r-biomart: Update to 2.52.0.

* gnu/packages/bioconductor.scm (r-biomart): Update to 2.52.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aa3438067c..aaa32b06f5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3052,13 +3052,13 @@ (define-public r-biobase
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.50.3")
+    (version "2.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1"))))
+                "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From e56181a34e5f4e814739f77eda21e13a8411bd63 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:36 +0200
Subject: gnu: r-biocparallel: Update to 1.30.2.

* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.30.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aaa32b06f5..a94105e68f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3090,13 +3090,13 @@ (define-public r-biomart
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.28.3")
+    (version "1.30.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0lkp7m2l66zq8yl788mkvi9kpb1haywxpf6ip9xl5y6iwm1w2b8p"))))
+                "0rqvwhs6d8ls1rq7j5ywl5k0qgblxpzimilyw335bi1yad5s10h3"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 6479274a0b5da9c80d5a7c565d4988b8860c970d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:36 +0200
Subject: gnu: r-biovizbase: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-biovizbase): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a94105e68f..cefc73ca7b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3171,14 +3171,14 @@ (define-public r-biostrings
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biovizBase" version))
        (sha256
         (base32
-         "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz"))))
+         "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
     (properties `((upstream-name . "biovizBase")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 417481b3b0ef331bca789e3adad9ee7084aa5fba Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:36 +0200
Subject: gnu: r-bsgenome: Update to 1.64.0.

* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.64.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cefc73ca7b..72e7f7f1ea 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3213,13 +3213,13 @@ (define-public r-biovizbase
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.62.0")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi"))))
+                "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From b7f95b40a86a2884b2b8e72e01b2888958265206 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:36 +0200
Subject: gnu: r-category: Update to 2.62.0.

* gnu/packages/bioconductor.scm (r-category): Update to 2.62.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 72e7f7f1ea..e39405eef0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3244,14 +3244,14 @@ (define-public r-bsgenome
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.60.0")
+    (version "2.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427"))))
+         "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 5e9e69ccd8020629bd68651feedaaeb03b908054 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:37 +0200
Subject: gnu: r-chipseeker: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-chipseeker): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e39405eef0..12e336caab 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3275,13 +3275,13 @@ (define-public r-category
 (define-public r-chipseeker
   (package
     (name "r-chipseeker")
-    (version "1.30.3")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ChIPseeker" version))
               (sha256
                (base32
-                "1f9m1p1viiigkmv15r2mknjrfw047jw1fylpqz5ipigc3jrphj1g"))))
+                "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From d66077a5ad9d2073a529ceee4594c117d66bd628 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:37 +0200
Subject: gnu: r-chipseq: Update to 1.46.0.

* gnu/packages/bioconductor.scm (r-chipseq): Update to 1.46.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 12e336caab..7c25d97adf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3321,14 +3321,14 @@ (define-public r-chipseeker
 (define-public r-chipseq
   (package
     (name "r-chipseq")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chipseq" version))
        (sha256
         (base32
-         "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6"))))
+         "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
-- 
cgit v1.2.3


From d15ab4ed30527d9d6f25a03d6973efdca501f56f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:37 +0200
Subject: gnu: r-complexheatmap: Update to 2.12.0.

* gnu/packages/bioconductor.scm (r-complexheatmap): Update to 2.12.0.
[propagated-inputs]: Add r-codetools.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c25d97adf..2f6b085558 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3347,20 +3347,21 @@ (define-public r-chipseq
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ComplexHeatmap" version))
        (sha256
         (base32
-         "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn"))))
+         "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65"))))
     (properties
      `((upstream-name . "ComplexHeatmap")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-circlize
            r-clue
+           r-codetools
            r-colorspace
            r-digest
            r-doparallel
-- 
cgit v1.2.3


From d29abfbd40735e41f33f394c3cafd97ffd3bd674 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:37 +0200
Subject: gnu: r-copywriter: Update to 2.28.0.

* gnu/packages/bioconductor.scm (r-copywriter): Update to 2.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2f6b085558..af4640eb47 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3387,14 +3387,14 @@ (define-public r-complexheatmap
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopywriteR" version))
        (sha256
         (base32
-         "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy"))))
+         "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
     (properties `((upstream-name . "CopywriteR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a83d8ee1eb325e7fa5ecd5cf47d0a4bf8ea426b1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:37 +0200
Subject: gnu: r-deseq2: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index af4640eb47..bd09bae583 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3458,14 +3458,14 @@ (define-public r-deseq
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9"))))
+         "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From ea0c72bed0109211145e0b50e28a754677da0a10 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:37 +0200
Subject: gnu: r-dexseq: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-dexseq): Update to 1.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bd09bae583..827d82e26f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3496,14 +3496,14 @@ (define-public r-deseq2
 (define-public r-dexseq
   (package
     (name "r-dexseq")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DEXSeq" version))
        (sha256
         (base32
-         "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1"))))
+         "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
     (properties `((upstream-name . "DEXSeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 380384a209535e6b33408bad306b88bd6582ee07 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:37 +0200
Subject: gnu: r-diffcyt: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-diffcyt): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 827d82e26f..96dded4bcc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3541,13 +3541,13 @@ (define-public r-dexseq
 (define-public r-diffcyt
   (package
     (name "r-diffcyt")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "diffcyt" version))
        (sha256
-        (base32 "1yc9mlc0ifb7h6rzskq97bsdq1kwdp5qq9l9mciwyxf6yjkmv5ni"))))
+        (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
     (properties `((upstream-name . "diffcyt")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 12a8b7bca3c92f7718192dd1849603a60ed0b391 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:38 +0200
Subject: gnu: r-dirichletmultinomial: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-dirichletmultinomial): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 96dded4bcc..70a81cf35a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3579,14 +3579,14 @@ (define-public r-diffcyt
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DirichletMultinomial" version))
        (sha256
         (base32
-         "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6"))))
+         "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
     (properties
      `((upstream-name . "DirichletMultinomial")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 1d19d45fe7373f5aec3a937b4c74827e99d39baa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:38 +0200
Subject: gnu: r-edaseq: Update to 2.30.0.

* gnu/packages/bioconductor.scm (r-edaseq): Update to 2.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 70a81cf35a..dea0dd42de 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3606,14 +3606,14 @@ (define-public r-dirichletmultinomial
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EDASeq" version))
        (sha256
         (base32
-         "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7"))))
+         "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
     (properties `((upstream-name . "EDASeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 9d030069d45593902c2bd0a4ddca8ee0bc427094 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:38 +0200
Subject: gnu: r-edger: Update to 3.38.1.

* gnu/packages/bioconductor.scm (r-edger): Update to 3.38.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dea0dd42de..a747353f6f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3646,13 +3646,13 @@ (define-public r-edaseq
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.36.0")
+    (version "3.38.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk"))))
+                "1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 89b669ba0e9554f8acead4873ea834be4cb9a891 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:38 +0200
Subject: gnu: r-ensembldb: Update to 2.20.1.

* gnu/packages/bioconductor.scm (r-ensembldb): Update to 2.20.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a747353f6f..6eed1808a7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3671,14 +3671,14 @@ (define-public r-edger
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.18.4")
+    (version "2.20.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1nsdcsghhh3ikv0hbn1aazdam7a6pqf1p6rz68ll2h6965kl4qzp"))))
+         "183rs74ngfvn9xz36csch495pqaash90yhhikm73m7b2bc37ziwz"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From b604766021012ce8bc0762b60930687ee9db0301 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:38 +0200
Subject: gnu: r-fastseg: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-fastseg): Update to 1.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6eed1808a7..11ed46fe4e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3716,14 +3716,14 @@ (define-public r-ensembldb
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fastseg" version))
        (sha256
         (base32
-         "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80"))))
+         "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-biocgenerics r-genomicranges r-iranges
-- 
cgit v1.2.3


From 3fd4c8f29f2312b335922d318c800e99879d6c11 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:38 +0200
Subject: gnu: r-gage: Update to 2.46.0.

* gnu/packages/bioconductor.scm (r-gage): Update to 2.46.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 11ed46fe4e..4ec4e2aef7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3743,14 +3743,14 @@ (define-public r-fastseg
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.44.0")
+    (version "2.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar"))))
+         "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi r-go-db r-graph r-keggrest))
-- 
cgit v1.2.3


From cb6e76dc6306bc0ff3cd60f02ad55ea5bb645223 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:39 +0200
Subject: gnu: r-genefilter: Update to 1.78.0.

* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.78.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4ec4e2aef7..aa983861a0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3771,14 +3771,14 @@ (define-public r-gage
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.76.0")
+    (version "1.78.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2"))))
+         "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran r-knitr))
-- 
cgit v1.2.3


From b755e0d623c7ad3ada96c5a4b3d57179fff0762d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:39 +0200
Subject: gnu: r-geneoverlap: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aa983861a0..c86da42aee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3795,13 +3795,13 @@ (define-public r-genefilter
 (define-public r-geneoverlap
   (package
     (name "r-geneoverlap")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GeneOverlap" version))
               (sha256
                (base32
-                "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm"))))
+                "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rcolorbrewer r-gplots))
-- 
cgit v1.2.3


From 09ae5950163d0fb8b93f5ee82d8199728ef04b3d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:39 +0200
Subject: gnu: r-genomation: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-genomation): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c86da42aee..0d5bcd004f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3814,13 +3814,13 @@ (define-public r-geneoverlap
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j"))))
+                "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
-- 
cgit v1.2.3


From 4966e9e9256382578d8f2935e5c3f6a20b4f1a4f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:39 +0200
Subject: gnu: r-genomeinfodb: Update to 1.32.2.

* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.32.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0d5bcd004f..9e96a71fc5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3861,13 +3861,13 @@ (define-public r-genomation
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.30.1")
+    (version "1.32.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55"))))
+                "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 1a04133411c0622028a9ed84d7a5195cd1aa41d2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:39 +0200
Subject: gnu: r-genomicalignments: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-genomicalignments): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9e96a71fc5..0196aafe35 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3888,13 +3888,13 @@ (define-public r-genomeinfodb
 (define-public r-genomicalignments
   (package
     (name "r-genomicalignments")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicAlignments" version))
               (sha256
                (base32
-                "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9"))))
+                "1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi"))))
     (properties
      `((upstream-name . "GenomicAlignments")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From fa516541c3a7cea51150961e275e45f60bb97153 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:39 +0200
Subject: gnu: r-genomicfeatures: Update to 1.48.1.

* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.48.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0196aafe35..2ade269bd4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3921,13 +3921,13 @@ (define-public r-genomicalignments
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.46.5")
+    (version "1.48.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1fhahqh87cikfrwqkm2z4nq3jyi530qvsbmf09j2hyhsm87hhrgg"))))
+                "18ain5s0ry6w0ki4c0czvwax2ncigrldyac30a6mlbzyaga6i54h"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From d14aeab8b84f0f2f8be2635c7eb1988a020c0a1a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:39 +0200
Subject: gnu: r-genomicfiles: Update to 1.32.1.

* gnu/packages/bioconductor.scm (r-genomicfiles): Update to 1.32.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2ade269bd4..bb3d945ac5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3965,14 +3965,14 @@ (define-public r-genomicfeatures
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-    (version "1.30.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicFiles" version))
        (sha256
         (base32
-         "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x"))))
+         "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
     (properties `((upstream-name . "GenomicFiles")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From bf93ff28c589c0b78c6a1c84ce342eb5803e315d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:40 +0200
Subject: gnu: r-genomicranges: Update to 1.48.0.

* gnu/packages/bioconductor.scm (r-genomicranges): Update to 1.48.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bb3d945ac5..61dcee02ea 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3999,13 +3999,13 @@ (define-public r-genomicfiles
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.46.1")
+    (version "1.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx"))))
+                "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 5c3a303d308ec87f08ef0ddf3f9b7096a241462b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:40 +0200
Subject: gnu: r-gostats: Update to 2.62.0.

* gnu/packages/bioconductor.scm (r-gostats): Update to 2.62.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 61dcee02ea..d1fec5992f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4026,14 +4026,14 @@ (define-public r-genomicranges
 (define-public r-gostats
   (package
     (name "r-gostats")
-    (version "2.60.0")
+    (version "2.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOstats" version))
        (sha256
         (base32
-         "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z"))))
+         "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
     (properties `((upstream-name . "GOstats")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3e1dbcb3bf44cc902caa94a2d84991f1f754f78e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:40 +0200
Subject: gnu: r-gseabase: Update to 1.58.0.

* gnu/packages/bioconductor.scm (r-gseabase): Update to 1.58.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d1fec5992f..e69149405b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4057,14 +4057,14 @@ (define-public r-gostats
 (define-public r-gseabase
   (package
     (name "r-gseabase")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GSEABase" version))
        (sha256
         (base32
-         "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6"))))
+         "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
     (properties `((upstream-name . "GSEABase")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3daf94f147f9ae3fb3416f004e43927faab75e36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:40 +0200
Subject: gnu: r-hpar: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-hpar): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e69149405b..23af48be71 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4086,14 +4086,14 @@ (define-public r-gseabase
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76"))))
+         "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From bb2b2f6543988702b70e0b1ff9ff0570ee417156 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:40 +0200
Subject: gnu: r-rhtslib: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-rhtslib): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 23af48be71..b2ea841270 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4106,14 +4106,14 @@ (define-public r-hpar
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4"))))
+         "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
-- 
cgit v1.2.3


From cd9b5f002956de52be1a4b26c860d480d89fe5cd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:40 +0200
Subject: gnu: r-impute: Update to 1.70.0.

* gnu/packages/bioconductor.scm (r-impute): Update to 1.70.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b2ea841270..ceb97ef88e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4135,13 +4135,13 @@ (define-public r-rhtslib
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.68.0")
+    (version "1.70.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5"))))
+                "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
     (native-inputs
      (list gfortran))
     (build-system r-build-system)
-- 
cgit v1.2.3


From a6cb10afc359666bffa47490484db66150dc02e5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:40 +0200
Subject: gnu: r-interactivedisplaybase: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-interactivedisplaybase): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ceb97ef88e..d9438bb959 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4155,14 +4155,14 @@ (define-public r-impute
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "interactiveDisplayBase" version))
        (sha256
         (base32
-         "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab"))))
+         "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
     (properties
      `((upstream-name . "interactiveDisplayBase")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 2a3372953d88fcc7bdf5f740aafac75633918bd0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:41 +0200
Subject: gnu: r-keggrest: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-keggrest): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d9438bb959..f9c6f6f8ba 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4180,14 +4180,14 @@ (define-public r-interactivedisplaybase
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279"))))
+         "0hzlm6nzmx0iyjh063512a3ghc1xqb58g5z2bnd2wl4y42iww7bg"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From cb17da65a5c2241d7cfb29f3d98a77ed8b70441c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:41 +0200
Subject: gnu: r-lfa: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-lfa): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f9c6f6f8ba..1490a0e3d5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4204,13 +4204,13 @@ (define-public r-keggrest
 (define-public r-lfa
   (package
     (name "r-lfa")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lfa" version))
        (sha256
-        (base32 "02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr"))))
+        (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
     (properties `((upstream-name . "lfa")))
     (build-system r-build-system)
     (propagated-inputs (list r-corpcor))
-- 
cgit v1.2.3


From 0cb9ffc4e3475b6f43451c1d06bfe6742b63413b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:41 +0200
Subject: gnu: r-limma: Update to 3.52.1.

* gnu/packages/bioconductor.scm (r-limma): Update to 3.52.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1490a0e3d5..9db0e78df0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4225,13 +4225,13 @@ (define-public r-lfa
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.50.3")
+    (version "3.52.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1p46sif1aygmw2p8ifiylxrrbfbgvcsa0zp40nxlxawc7h56rybp"))))
+                "193l3z2jv0kr91nl4r64p3jzb2rai9k8akx1zw7303nsnwpiiaay"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
-- 
cgit v1.2.3


From 56741afedd88dbf3fe6bca566b88a9af19c52a5f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:41 +0200
Subject: gnu: r-methylkit: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-methylkit): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9db0e78df0..b422b5d601 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4244,13 +4244,13 @@ (define-public r-limma
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx"))))
+                "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8ec1ca001d2494e3f024aa1a4428bb2183bb7551 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:41 +0200
Subject: gnu: r-mutationalpatterns: Update to 3.6.0.

* gnu/packages/bioconductor.scm (r-mutationalpatterns): Update to 3.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b422b5d601..86a5895811 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4318,14 +4318,14 @@ (define-public r-motifrg
 (define-public r-mutationalpatterns
   (package
     (name "r-mutationalpatterns")
-    (version "3.4.1")
+    (version "3.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MutationalPatterns" version))
        (sha256
         (base32
-         "0i6fq6736gvrqn45r7nrhl0ns45qwj1bl4yc6qlalw2g46mjxf6k"))))
+         "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From d6f683b561aa2ed7b8a9ffacc33c1a8b414099ce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:41 +0200
Subject: gnu: r-msnbase: Update to 2.22.0.

* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 86a5895811..28ca320fad 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4364,14 +4364,14 @@ (define-public r-mutationalpatterns
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.20.4")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0d3b0i154dyz1wvy2jwf5831bzbmalw7rzvxj8rd7658zjhghgzc"))))
+         "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d6fe1e2d120e4254c3c0b50420756fa5c29374c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:42 +0200
Subject: gnu: r-msnid: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-msnid): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 28ca320fad..8b99fecef1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4409,14 +4409,14 @@ (define-public r-msnbase
 (define-public r-msnid
   (package
     (name "r-msnid")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnID" version))
        (sha256
         (base32
-         "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p"))))
+         "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
     (properties `((upstream-name . "MSnID")))
     (build-system r-build-system)
     (arguments
-- 
cgit v1.2.3


From 3eb763c2bad4eeecc080656ce04ecd3ed858e0dc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:42 +0200
Subject: gnu: r-mzid: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-mzid): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8b99fecef1..3daec56401 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4466,14 +4466,14 @@ (define-public r-msnid
 (define-public r-mzid
   (package
     (name "r-mzid")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzID" version))
        (sha256
         (base32
-         "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri"))))
+         "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
     (properties `((upstream-name . "mzID")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d1134b61fda491037e33364ef19183ec360d0854 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:42 +0200
Subject: gnu: r-mzr: Update to 2.30.0.

* gnu/packages/bioconductor.scm (r-mzr): Update to 2.30.0.
[propagated-inputs]: Remove r-zlibbioc.
[inputs]: Replace boost-for-mysql with boost.
---
 gnu/packages/bioconductor.scm | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3daec56401..eab73f7f05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4497,19 +4497,17 @@ (define-public r-mzid
 (define-public r-mzr
   (package
     (name "r-mzr")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1"))
+         "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
        (modules '((guix build utils)))
        (snippet
-        '(begin
-           (delete-file-recursively "src/boost")
-           #t))))
+        '(delete-file-recursively "src/boost"))))
     (properties `((upstream-name . "mzR")))
     (build-system r-build-system)
     (arguments
@@ -4523,12 +4521,9 @@ (define-public r-mzr
                (("\\ARCH_OBJS=" line)
                 (string-append line
                                "\nBOOST_LIBS=-lboost_system -lboost_regex \
--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
-             #t)))))
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
     (inputs
-     (list ;; Our default boost package won't work here, unfortunately, even with
-           ;; mzR version 2.28.0.
-           boost-for-mysql ; use this instead of the bundled boost sources
+     (list boost ; use this instead of the bundled boost sources
            zlib))
     (propagated-inputs
      (list r-biobase
@@ -4536,8 +4531,7 @@ (define-public r-mzr
            r-ncdf4
            r-protgenerics
            r-rcpp
-           r-rhdf5lib
-           r-zlibbioc))
+           r-rhdf5lib))
     (native-inputs
      (list r-knitr))
     (home-page "https://github.com/sneumann/mzR/")
-- 
cgit v1.2.3


From e3878bc3c075c0ec9cc75cde7df839521b6ddf56 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:42 +0200
Subject: gnu: r-organismdbi: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-organismdbi): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eab73f7f05..0e33da51ac 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4548,14 +4548,14 @@ (define-public r-mzr
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OrganismDbi" version))
        (sha256
         (base32
-         "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83"))))
+         "1xklaiyd4mv9sf9211flq1s68fhdn53y2i4l1k2ib39a4l6y9cyr"))))
     (properties `((upstream-name . "OrganismDbi")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d4201b5f6185235737be4ca35b5d984023ed5377 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:42 +0200
Subject: gnu: r-pcamethods: Update to 1.88.0.

* gnu/packages/bioconductor.scm (r-pcamethods): Update to 1.88.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0e33da51ac..116359fcd6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4580,14 +4580,14 @@ (define-public r-organismdbi
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
-    (version "1.86.0")
+    (version "1.88.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pcaMethods" version))
        (sha256
         (base32
-         "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg"))))
+         "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
     (properties `((upstream-name . "pcaMethods")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 2b7c604ebff15a1e326e24373260ddaeccac408d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:42 +0200
Subject: gnu: r-protgenerics: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-protgenerics): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 116359fcd6..bcf4127a4b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4649,14 +4649,14 @@ (define-public r-pscbs
 (define-public r-protgenerics
   (package
     (name "r-protgenerics")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ProtGenerics" version))
        (sha256
         (base32
-         "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0"))))
+         "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
     (properties `((upstream-name . "ProtGenerics")))
     (build-system r-build-system)
     (home-page "https://github.com/lgatto/ProtGenerics")
-- 
cgit v1.2.3


From 1a873db6b28dfb816854749d19b0abd5a7e895dd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:42 +0200
Subject: gnu: r-rbgl: Update to 1.72.0.

* gnu/packages/bioconductor.scm (r-rbgl): Update to 1.72.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bcf4127a4b..36d3389845 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4669,14 +4669,14 @@ (define-public r-protgenerics
 (define-public r-rbgl
   (package
     (name "r-rbgl")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RBGL" version))
        (sha256
         (base32
-         "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0"))))
+         "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
     (properties `((upstream-name . "RBGL")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 9d05a948ea144200b0ddc27dc1fe3058dc97ed09 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:43 +0200
Subject: gnu: r-rcas: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-rcas): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 36d3389845..9edb17f78f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4691,13 +4691,13 @@ (define-public r-rbgl
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "RCAS" version))
               (sha256
                (base32
-                "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7"))))
+                "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
     (properties `((upstream-name . "RCAS")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 21669d75f6844f8fd3a469a9bbd4b29e9dae0706 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:43 +0200
Subject: gnu: r-regioner: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-regioner): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9edb17f78f..9e6ba1f1f9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4741,14 +4741,14 @@ (define-public r-rcas
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.26.1")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p"))))
+         "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From de8b8c86e628e724db4867b898e000c7c067fb78 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:43 +0200
Subject: gnu: r-reportingtools: Update to 2.36.0.

* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9e6ba1f1f9..f639211c9f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4772,14 +4772,14 @@ (define-public r-regioner
 (define-public r-reportingtools
   (package
     (name "r-reportingtools")
-    (version "2.34.0")
+    (version "2.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReportingTools" version))
        (sha256
         (base32
-         "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7"))))
+         "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
     (properties
      `((upstream-name . "ReportingTools")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3c31e7e249403385441bb7bd0e47fc9cb5ddcf98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:43 +0200
Subject: gnu: r-rhdf5: Update to 2.40.0.

* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.40.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f639211c9f..6aa58f17e3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4822,13 +4822,13 @@ (define-public r-reportingtools
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.38.1")
+    (version "2.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "1mlwp7bblhbpmd90sxj02zpq1q3fyg8v7ankyjb1y284xaymp02y"))))
+                "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-rhdf5filters r-rhdf5lib))
-- 
cgit v1.2.3


From a8c63ab6103201d57b0da82a773f942a5cfccabb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:43 +0200
Subject: gnu: r-rhdf5filters: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6aa58f17e3..3869f6f7eb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4849,14 +4849,14 @@ (define-public r-rhdf5
 (define-public r-rhdf5filters
   (package
     (name "r-rhdf5filters")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rhdf5filters" version))
        (sha256
         (base32
-         "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78"))))
+         "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
     (properties `((upstream-name . "rhdf5filters")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 990ee0c7ccf2fb2253831a38405fa1afba56fea6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:43 +0200
Subject: gnu: r-rsamtools: Update to 2.12.0.

* gnu/packages/bioconductor.scm (r-rsamtools): Update to 2.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3869f6f7eb..39354a5e23 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4875,13 +4875,13 @@ (define-public r-rhdf5filters
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.10.0")
+    (version "2.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh"))))
+                "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From ea283a3cda0089937baa8c43c3d9447673bfe8c2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:44 +0200
Subject: gnu: r-rtracklayer: Update to 1.56.0.

* gnu/packages/bioconductor.scm (r-rtracklayer): Update to 1.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 39354a5e23..c73f63955c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4940,13 +4940,13 @@ (define-public r-restfulr
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.54.0")
+    (version "1.56.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc"))))
+                "1d9sak1xrrkcvj0q3vnp6w2k0nx2k2ajhsbq0dyb4nhcghp5w8fd"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 021ab21b578cd2b6476fc8997904c2ea95a01d3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:44 +0200
Subject: gnu: r-scannotatr: Update to 1.2.0.

* gnu/packages/bioconductor.scm (r-scannotatr): Update to 1.2.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c73f63955c..0a5329b193 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5019,13 +5019,13 @@ (define-public r-samr
 (define-public r-scannotatr
   (package
     (name "r-scannotatr")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scAnnotatR" version))
        (sha256
-        (base32 "08jq04ckjw8a5y753almc5bl8vnn4j6qp2zb7bb9w3ql3ddy7b21"))))
+        (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
     (properties `((upstream-name . "scAnnotatR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a260fc5a905c5fae03259511be1ced4524d0686d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:44 +0200
Subject: gnu: r-scdblfinder: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-scdblfinder): Update to 1.10.0.
[propagated-inputs]: Add r-genomeinfodb, r-genomicranges, r-iranges, r-rsamtools, and
r-rtracklayer.
---
 gnu/packages/bioconductor.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0a5329b193..d42d838133 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5056,13 +5056,13 @@ (define-public r-scannotatr
 (define-public r-scdblfinder
   (package
     (name "r-scdblfinder")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDblFinder" version))
        (sha256
-        (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd"))))
+        (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
     (properties `((upstream-name . "scDblFinder")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5072,9 +5072,14 @@ (define-public r-scdblfinder
            r-biocsingular
            r-bluster
            r-delayedarray
+           r-genomeinfodb
+           r-genomicranges
            r-igraph
+           r-iranges
            r-mass
            r-matrix
+           r-rsamtools
+           r-rtracklayer
            r-s4vectors
            r-scater
            r-scran
-- 
cgit v1.2.3


From 5346b424cccfa3cb5d10c73d880ca60a239e35fc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:44 +0200
Subject: gnu: r-seqlogo: Update to 1.62.0.

* gnu/packages/bioconductor.scm (r-seqlogo): Update to 1.62.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d42d838133..bfafe4451b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5101,14 +5101,14 @@ (define-public r-scdblfinder
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqLogo" version))
        (sha256
         (base32
-         "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl"))))
+         "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
     (properties `((upstream-name . "seqLogo")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From 27588f020d00efbd2638695f39743bb1a5abd942 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:44 +0200
Subject: gnu: r-seqpattern: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-seqpattern): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bfafe4451b..fc6802ee0f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5124,13 +5124,13 @@ (define-public r-seqlogo
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "seqPattern" version))
               (sha256
                (base32
-                "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na"))))
+                "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
     (properties
      `((upstream-name . "seqPattern")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 6d2b2e0ad98675a266c23586567726da9dd67d24 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:44 +0200
Subject: gnu: r-shortread: Update to 1.54.0.

* gnu/packages/bioconductor.scm (r-shortread): Update to 1.54.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fc6802ee0f..dbcb63ab08 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5147,14 +5147,14 @@ (define-public r-seqpattern
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx"))))
+         "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From 9b935eaa562a7d60d2bd6b4c09f2f327eb254f2b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:45 +0200
Subject: gnu: r-simplifyenrichment: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-simplifyenrichment): Update to 1.6.0.
[propagated-inputs]: Add r-colorspace and r-globaloptions.
---
 gnu/packages/bioconductor.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dbcb63ab08..4f437d271b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5190,14 +5190,14 @@ (define-public r-shortread
 (define-public r-simplifyenrichment
   (package
     (name "r-simplifyenrichment")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "simplifyEnrichment" version))
        (sha256
         (base32
-         "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98"))))
+         "1g3kfa17p60jkk4l34vc5hdq83w082qsxbjvpqw7r9rdd8d79z2q"))))
     (properties
      `((upstream-name . "simplifyEnrichment")))
     (build-system r-build-system)
@@ -5207,9 +5207,11 @@ (define-public r-simplifyenrichment
            r-circlize
            r-clue
            r-cluster
+           r-colorspace
            r-complexheatmap
            r-digest
            r-getoptlong
+           r-globaloptions
            r-go-db
            r-gosemsim
            r-matrix
-- 
cgit v1.2.3


From 909d580b9aa43414b0f75331467b0cf24e103001 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:45 +0200
Subject: gnu: r-transcriptr: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-transcriptr): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f437d271b..a58d4954f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5231,13 +5231,13 @@ (define-public r-simplifyenrichment
 (define-public r-transcriptr
   (package
     (name "r-transcriptr")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "transcriptR" version))
        (sha256
-        (base32 "1p5l2z3szx3qh02x7r81ajl7yc5wqsri6q6pzw83livmalcli5yy"))))
+        (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
     (properties `((upstream-name . "transcriptR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3f873a27e0c5f0c7cd5c9865d9c1a9a052af0b84 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:45 +0200
Subject: gnu: r-trajectoryutils: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-trajectoryutils): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a58d4954f1..d7121c3708 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5281,14 +5281,14 @@ (define-public r-transcriptr
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TrajectoryUtils" version))
        (sha256
         (base32
-         "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1"))))
+         "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
     (properties
      `((upstream-name . "TrajectoryUtils")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 8d1ab3f57d31be4e4a09232eed08bf79f9884746 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:45 +0200
Subject: gnu: r-slingshot: Update to 2.4.0.

* gnu/packages/bioconductor.scm (r-slingshot): Update to 2.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d7121c3708..02ded68662 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5308,13 +5308,13 @@ (define-public r-trajectoryutils
 (define-public r-slingshot
   (package
    (name "r-slingshot")
-   (version "2.2.1")
+   (version "2.4.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "slingshot" version))
             (sha256
              (base32
-              "10kjpmckhzjf41yfhzg7c8idqa9cxz33r4rza6rwihnqnw1liff3"))))
+              "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-igraph
-- 
cgit v1.2.3


From ed19cbbf15b2b5f9530b3093c4b7ae6275d114b4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:45 +0200
Subject: gnu: r-stager: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-stager): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 02ded68662..fc26df4d82 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5340,13 +5340,13 @@ (define-public r-slingshot
 (define-public r-stager
   (package
     (name "r-stager")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "stageR" version))
        (sha256
-        (base32 "0vpx0v04hgkhzi0bm7ipnb9xr37n5wvnnr45lljgni8pwabfkf6y"))))
+        (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
     (properties `((upstream-name . "stageR")))
     (build-system r-build-system)
     (propagated-inputs (list r-summarizedexperiment))
-- 
cgit v1.2.3


From d044d62102711c8a9ba36086c42108665ff3360a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:45 +0200
Subject: gnu: r-stringdb: Update to 2.8.4.

* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.8.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fc26df4d82..28494b828d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5363,13 +5363,13 @@ (define-public r-stager
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-    (version "2.6.5")
+    (version "2.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "STRINGdb" version))
        (sha256
-        (base32 "0n2r2zc2sx1a2a8wqqxz6z7i4ynaj18iwbwgif7469n13agji5mv"))))
+        (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
     (properties `((upstream-name . "STRINGdb")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 803722761790eab8b4518c865e5c698f11c2ea5e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:45 +0200
Subject: gnu: r-structuralvariantannotation: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-structuralvariantannotation): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 28494b828d..6f96758cbd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5396,13 +5396,13 @@ (define-public r-stringdb
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")
-    (version "1.10.1")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "StructuralVariantAnnotation" version))
        (sha256
-        (base32 "009l27kb9gvwwf57dwxfribhfhvn4z5pw8yc847l6pkbzqggx678"))))
+        (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
-- 
cgit v1.2.3


From a0734f8bdd354ff4afc7fb0bda57e629f431e9c4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:46 +0200
Subject: gnu: r-summarizedexperiment: Update to 1.26.1.

* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.26.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6f96758cbd..2fd092dbf0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5433,13 +5433,13 @@ (define-public r-structuralvariantannotation
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.24.0")
+    (version "1.26.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a"))))
+                "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 02c26f40b7f7b90e5a3ffe231cf1f93666acf1b2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:46 +0200
Subject: gnu: r-sva: Update to 3.44.0.

* gnu/packages/bioconductor.scm (r-sva): Update to 3.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2fd092dbf0..009e0c2c6e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5467,14 +5467,14 @@ (define-public r-summarizedexperiment
 (define-public r-sva
   (package
     (name "r-sva")
-    (version "3.42.0")
+    (version "3.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sva" version))
        (sha256
         (base32
-         "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj"))))
+         "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-edger
-- 
cgit v1.2.3


From de403d02ad89c58dbbf9b709411ce2e2b4d197aa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:46 +0200
Subject: gnu: r-systempiper: Update to 2.2.2.

* gnu/packages/bioconductor.scm (r-systempiper): Update to 2.2.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 009e0c2c6e..6f860c8283 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5498,14 +5498,14 @@ (define-public r-sva
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.0.8")
+    (version "2.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "0ajlw9yg6fha76rkkmsk5niq99s33k9437bkgi9whgh3pa6bkab2"))))
+         "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 47cdb428405722277fc3be3513191c52d91279ce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:46 +0200
Subject: gnu: r-topgo: Update to 2.48.0.

* gnu/packages/bioconductor.scm (r-topgo): Update to 2.48.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6f860c8283..b612afa42e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5541,13 +5541,13 @@ (define-public r-systempiper
 (define-public r-topgo
   (package
     (name "r-topgo")
-    (version "2.46.0")
+    (version "2.48.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "topGO" version))
               (sha256
                (base32
-                "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2"))))
+                "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
     (properties
      `((upstream-name . "topGO")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 131135458e696b55824e77c0639e5b3d3f93f7e4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:46 +0200
Subject: gnu: r-tximport: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-tximport): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b612afa42e..17523b2971 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5574,13 +5574,13 @@ (define-public r-topgo
 (define-public r-tximport
   (package
     (name "r-tximport")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tximport" version))
               (sha256
                (base32
-                "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4"))))
+                "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From a9d0efc639c3a79d5a8f98e52044077dc6b75af1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:46 +0200
Subject: gnu: r-variantannotation: Update to 1.42.1.

* gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.42.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 17523b2971..ce0eb1bb51 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5631,13 +5631,13 @@ (define-public r-valr
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.40.0")
+    (version "1.42.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva"))))
+                "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (propagated-inputs
-- 
cgit v1.2.3


From be389d989dd508704ef4df4dec06f86d9c46a148 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:46 +0200
Subject: gnu: r-vsn: Update to 3.64.0.

* gnu/packages/bioconductor.scm (r-vsn): Update to 3.64.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ce0eb1bb51..b74f2c1e2a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5669,14 +5669,14 @@ (define-public r-variantannotation
 (define-public r-vsn
   (package
     (name "r-vsn")
-    (version "3.62.0")
+    (version "3.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "vsn" version))
        (sha256
         (base32
-         "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x"))))
+         "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
-- 
cgit v1.2.3


From e7a0b1411599b35f45de75a484ff5869d530b7ee Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:47 +0200
Subject: gnu: r-xina: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-xina): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b74f2c1e2a..bc8c5c76ef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5738,13 +5738,13 @@ (define-public r-xcir
 (define-public r-xina
   (package
     (name "r-xina")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "XINA" version))
        (sha256
-        (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp"))))
+        (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
     (properties `((upstream-name . "XINA")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 036dcaed7dd6714668202edde469d4a38ac14002 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:47 +0200
Subject: gnu: r-xmapbridge: Update to 1.54.0.

* gnu/packages/bioconductor.scm (r-xmapbridge): Update to 1.54.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bc8c5c76ef..8428a49aaf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5774,13 +5774,13 @@ (define-public r-xina
 (define-public r-xmapbridge
   (package
     (name "r-xmapbridge")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xmapbridge" version))
        (sha256
-        (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi"))))
+        (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
     (properties `((upstream-name . "xmapbridge")))
     (build-system r-build-system)
     (home-page "https://git.bioconductor.org/packages/xmapbridge")
-- 
cgit v1.2.3


From 2b36da17849146e5775e603a9e4562bc36542ba8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:47 +0200
Subject: gnu: r-xvector: Update to 0.36.0.

* gnu/packages/bioconductor.scm (r-xvector): Update to 0.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8428a49aaf..512957d4df 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5801,13 +5801,13 @@ (define-public r-xmapbridge
 (define-public r-xvector
   (package
     (name "r-xvector")
-    (version "0.34.0")
+    (version "0.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "XVector" version))
               (sha256
                (base32
-                "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0"))))
+                "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
     (properties
      `((upstream-name . "XVector")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 2bc32aa065bb2e86f328e694ad54572d0a4b8393 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:47 +0200
Subject: gnu: r-zlibbioc: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-zlibbioc): Update to 1.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 512957d4df..4ef9dfe6c9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5835,13 +5835,13 @@ (define-public r-xvector
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-    (version "1.40.0")
+    (version "1.42.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "zlibbioc" version))
               (sha256
                (base32
-                "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj"))))
+                "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
     (properties
      `((upstream-name . "zlibbioc")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 2b652812e8df0f59e0a76802226657013ba40c4d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:47 +0200
Subject: gnu: r-zellkonverter: Update to 1.6.1.

* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.6.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4ef9dfe6c9..ce227b3453 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5854,13 +5854,13 @@ (define-public r-zlibbioc
 (define-public r-zellkonverter
   (package
     (name "r-zellkonverter")
-    (version "1.4.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zellkonverter" version))
        (sha256
-        (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg"))))
+        (base32 "1w3qi35vk289cpky1pb0wgg1hr55s5kdw7np98i9c1vmwi3gvwr7"))))
     (properties `((upstream-name . "zellkonverter")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4268f796c8de69f0aee771ac2ef1429c1f8a8824 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:47 +0200
Subject: gnu: r-geneplotter: Update to 1.74.0.

* gnu/packages/bioconductor.scm (r-geneplotter): Update to 1.74.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ce227b3453..e01d2f4ef5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5886,14 +5886,14 @@ (define-public r-zellkonverter
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8"))))
+         "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
-- 
cgit v1.2.3


From 4ee5d02e70acdc43de6d3026886f2589fa2a2768 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:47 +0200
Subject: gnu: r-oligoclasses: Update to 1.58.0.

* gnu/packages/bioconductor.scm (r-oligoclasses): Update to 1.58.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e01d2f4ef5..835f9712fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5911,14 +5911,14 @@ (define-public r-geneplotter
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264"))))
+         "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8a2e344cf7c5b4d5397767ae3525f217d2f43d4a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:48 +0200
Subject: gnu: r-oligo: Update to 1.60.0.

* gnu/packages/bioconductor.scm (r-oligo): Update to 1.60.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 835f9712fd..0e7eecacc7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5946,14 +5946,14 @@ (define-public r-oligoclasses
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6"))))
+         "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs (list zlib))
-- 
cgit v1.2.3


From ec76f7ca9bdca96f11f06a554ca59f39e23d1e06 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:48 +0200
Subject: gnu: r-qvalue: Update to 2.28.0.

* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0e7eecacc7..6996d9037d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5982,14 +5982,14 @@ (define-public r-oligo
 (define-public r-qvalue
   (package
     (name "r-qvalue")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "qvalue" version))
        (sha256
         (base32
-         "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138"))))
+         "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-ggplot2 r-reshape2))
-- 
cgit v1.2.3


From 21db7a48e04b266ddd131ee4cca1cad263bf19ca Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:48 +0200
Subject: gnu: r-apeglm: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-apeglm): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6996d9037d..0287df0423 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6036,13 +6036,13 @@ (define r-rcppnumerical
 (define-public r-apeglm
   (package
    (name "r-apeglm")
-   (version "1.16.0")
+   (version "1.18.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "apeglm" version))
             (sha256
              (base32
-              "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr"))))
+              "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
    (properties `((upstream-name . "apeglm")))
    (build-system r-build-system)
    (propagated-inputs
-- 
cgit v1.2.3


From 84fc29bad68605b24ab4c0948e76f5380442108d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:48 +0200
Subject: gnu: r-greylistchip: Update to 1.28.1.

* gnu/packages/bioconductor.scm (r-greylistchip): Update to 1.28.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0287df0423..08731b742d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6063,13 +6063,13 @@ (define-public r-apeglm
 (define-public r-greylistchip
   (package
    (name "r-greylistchip")
-   (version "1.26.0")
+   (version "1.28.1")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "GreyListChIP" version))
             (sha256
              (base32
-              "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv"))))
+              "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
    (properties `((upstream-name . "GreyListChIP")))
    (build-system r-build-system)
    (propagated-inputs
-- 
cgit v1.2.3


From 7bc3e13bf5221b8e83afa5a5c2e92ffaec23de96 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:48 +0200
Subject: gnu: r-diffbind: Update to 3.6.1.

* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.6.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 08731b742d..afc5100c70 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6090,14 +6090,14 @@ (define-public r-greylistchip
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.4.11")
+    (version "3.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1xprj3x3s3yh6fwsdcl4zgfbhn640422x1lhhrmvdr836jr8sxcj"))))
+         "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From f6c66051021bd0f95b69f791043bc2771c53de27 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:48 +0200
Subject: gnu: r-mbkmeans: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-mbkmeans): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index afc5100c70..a75f13036b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6168,13 +6168,13 @@ (define-public r-ripseeker
 (define-public r-mbkmeans
   (package
     (name "r-mbkmeans")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "mbkmeans" version))
               (sha256
                (base32
-                "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k"))))
+                "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From de49b64b6945399faa7dda3026265ab16576a40d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:49 +0200
Subject: gnu: r-multtest: Update to 2.52.0.

* gnu/packages/bioconductor.scm (r-multtest): Update to 2.52.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a75f13036b..35137a2727 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6200,14 +6200,14 @@ (define-public r-mbkmeans
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.50.0")
+    (version "2.52.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns"))))
+         "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-survival r-biocgenerics r-biobase r-mass))
-- 
cgit v1.2.3


From d825e79fc849e0f3be03562ec49d098e957c1628 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:49 +0200
Subject: gnu: r-graph: Update to 1.74.0.

* gnu/packages/bioconductor.scm (r-graph): Update to 1.74.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 35137a2727..739219b151 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6235,13 +6235,13 @@ (define-public r-multtest
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0"))))
+                "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics))
-- 
cgit v1.2.3


From ef5c266f23098aa3aebbc61fc9321479f4818c8f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:49 +0200
Subject: gnu: r-chippeakanno: Update to 3.30.0.

* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 739219b151..c34da5c575 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6328,14 +6328,14 @@ (define-public r-codedepends
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.28.1")
+    (version "3.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw"))))
+         "1ch636j3zd6hcfnl455vjs36wffrdhwzyvkbikcwjg7idiknjdkf"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a1da6d7d45e9efc946212d51988b26f5616695fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:49 +0200
Subject: gnu: r-matrixgenerics: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c34da5c575..5676874ff5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6382,13 +6382,13 @@ (define-public r-chippeakanno
 (define-public r-matrixgenerics
   (package
    (name "r-matrixgenerics")
-   (version "1.6.0")
+   (version "1.8.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MatrixGenerics" version))
             (sha256
              (base32
-              "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3"))))
+              "0s7s39v9lqniirjgp8lbmffw0c8rsp6bndgzy1zlyh5vivfih0f5"))))
    (properties
     `((upstream-name . "MatrixGenerics")))
    (build-system r-build-system)
-- 
cgit v1.2.3


From a7c3f7f2b1079169b13aed00ba32749f9f64f53b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:49 +0200
Subject: gnu: r-marray: Update to 1.74.0.

* gnu/packages/bioconductor.scm (r-marray): Update to 1.74.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5676874ff5..cea0fa6f60 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6409,12 +6409,12 @@ (define-public r-matrixgenerics
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz"))))
+               (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-limma))
-- 
cgit v1.2.3


From 7188427b5c6ba5ab991c3db35a598e8bb879ad02 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:49 +0200
Subject: gnu: r-cghbase: Update to 1.56.0.

* gnu/packages/bioconductor.scm (r-cghbase): Update to 1.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cea0fa6f60..30d83e4c28 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6428,12 +6428,12 @@ (define-public r-marray
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.54.0")
+   (version "1.56.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d"))))
+             (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
-- 
cgit v1.2.3


From 3dd1b0508d54520eb0d655b112f79bc9d8f13547 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:50 +0200
Subject: gnu: r-cghcall: Update to 2.58.0.

* gnu/packages/bioconductor.scm (r-cghcall): Update to 2.58.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 30d83e4c28..fdabba3fd5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6447,12 +6447,12 @@ (define-public r-cghbase
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.56.0")
+   (version "2.58.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr"))))
+             (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
-- 
cgit v1.2.3


From ecd2d01d1e81924e1f40bef6c9a7ddf0889324cb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:50 +0200
Subject: gnu: r-qdnaseq: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fdabba3fd5..0531d3c1e0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6466,12 +6466,12 @@ (define-public r-cghcall
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj"))))
+               (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d6559d1e1b8b7a94305a62a3ab25f32b96a51ae5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:50 +0200
Subject: gnu: r-bayseq: Update to 2.30.0.

* gnu/packages/bioconductor.scm (r-bayseq): Update to 2.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0531d3c1e0..8f87da38d4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6498,14 +6498,14 @@ (define-public r-qdnaseq
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r"))))
+         "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d47ffaf7ee4661736ef122f6ad825deded9321a2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:50 +0200
Subject: gnu: r-chipcomp: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8f87da38d4..6b9a512a11 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6522,14 +6522,14 @@ (define-public r-bayseq
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq"))))
+         "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 2a8444ca5c0fce4afaf205ceef3f86c12088f2c5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:50 +0200
Subject: gnu: r-riboprofiling: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-riboprofiling): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6b9a512a11..b1f5a5d577 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6556,14 +6556,14 @@ (define-public r-chipcomp
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx"))))
+         "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 292efe0ae2db337beea30e0f4406d35829e42dc1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:50 +0200
Subject: gnu: r-riboseqr: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-riboseqr): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b1f5a5d577..ffc9282850 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6597,14 +6597,14 @@ (define-public r-riboprofiling
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd"))))
+         "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6695c4e33b821aab4c2026ae93718978577c01ce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:51 +0200
Subject: gnu: r-interactionset: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ffc9282850..38c16008fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6625,14 +6625,14 @@ (define-public r-riboseqr
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw"))))
+         "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 120329918b3e1657477ec433ba4dc915eb8c0d7e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:51 +0200
Subject: gnu: r-genomicinteractions: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 38c16008fd..519dc4aeb3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6659,14 +6659,14 @@ (define-public r-interactionset
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb"))))
+         "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 6d9a73c84717c6e1b669a61ac69d9a7b7d004083 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:51 +0200
Subject: gnu: r-ctc: Update to 1.70.0.

* gnu/packages/bioconductor.scm (r-ctc): Update to 1.70.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 519dc4aeb3..422cfc54be 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6700,14 +6700,14 @@ (define-public r-genomicinteractions
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx"))))
+         "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
     (build-system r-build-system)
     (propagated-inputs (list r-amap))
     (home-page "https://bioconductor.org/packages/ctc/")
-- 
cgit v1.2.3


From 53b152b2cf978082afa45cac71370d899c54e782 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:51 +0200
Subject: gnu: r-goseq: Update to 1.48.0.

* gnu/packages/bioconductor.scm (r-goseq): Update to 1.48.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 422cfc54be..3657de957e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6720,14 +6720,14 @@ (define-public r-ctc
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0"))))
+         "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From 09d473505553dbe161a053870a2bd8ca4e78b712 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:51 +0200
Subject: gnu: r-glimma: Update to 2.6.0.

* gnu/packages/bioconductor.scm (r-glimma): Update to 2.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3657de957e..1baf6d9660 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6746,14 +6746,14 @@ (define-public r-goseq
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "2.4.0")
+    (version "2.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9"))))
+         "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a028875b639fc2a2e941e0de7243fdff00fa46c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:51 +0200
Subject: gnu: r-rots: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-rots): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1baf6d9660..9f2749dff4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6779,14 +6779,14 @@ (define-public r-glimma
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki"))))
+         "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 86dd93110e17ad6f1a3ca1520d049ed83008c2ce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:52 +0200
Subject: gnu: r-plgem: Update to 1.68.0.

* gnu/packages/bioconductor.scm (r-plgem): Update to 1.68.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f2749dff4..28355296e3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6802,14 +6802,14 @@ (define-public r-rots
 (define-public r-plgem
   (package
     (name "r-plgem")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "plgem" version))
        (sha256
         (base32
-         "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3"))))
+         "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-mass))
-- 
cgit v1.2.3


From d6c3acb1c2bf774ef665ac64a4218607ce7cffaa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:52 +0200
Subject: gnu: r-inspect: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-inspect): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 28355296e3..02d5befe6f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6826,14 +6826,14 @@ (define-public r-plgem
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk"))))
+         "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8b475c3e92fe5da86e719cef7de7f10f6d9efcaf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:52 +0200
Subject: gnu: r-dnabarcodes: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-dnabarcodes): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 02d5befe6f..1076b5751c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6872,14 +6872,14 @@ (define-public r-inspect
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg"))))
+         "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0190978dcf73f224172ddd6d29134a1b909dd2fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:52 +0200
Subject: gnu: r-ruvseq: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-ruvseq): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1076b5751c..59b13dbd00 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6899,14 +6899,14 @@ (define-public r-dnabarcodes
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q"))))
+         "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From ccee3dcc6b33fc89fd0252b1756f3a0332f4606c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:52 +0200
Subject: gnu: r-biocneighbors: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 59b13dbd00..761b194dd2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6924,14 +6924,14 @@ (define-public r-ruvseq
 (define-public r-biocneighbors
   (package
     (name "r-biocneighbors")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocNeighbors" version))
        (sha256
         (base32
-         "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr"))))
+         "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
     (properties `((upstream-name . "BiocNeighbors")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 80266651911ac6ef08fad9f9d44d87b7bd7981a9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:52 +0200
Subject: gnu: r-scaledmatrix: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 761b194dd2..69f2830806 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6952,14 +6952,14 @@ (define-public r-biocneighbors
 (define-public r-scaledmatrix
   (package
     (name "r-scaledmatrix")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ScaledMatrix" version))
        (sha256
         (base32
-         "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc"))))
+         "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl"))))
     (properties `((upstream-name . "ScaledMatrix")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 21715b19d3448b036c490e5062e25a8c02b073f6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:53 +0200
Subject: gnu: r-treeio: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-treeio): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 69f2830806..def4da17bc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6978,14 +6978,14 @@ (define-public r-scaledmatrix
 (define-public r-treeio
   (package
     (name "r-treeio")
-    (version "1.18.1")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "treeio" version))
        (sha256
         (base32
-         "19i8jhvycv57zbxhpn5gx5ymdiws64kc3nidc00xh1j9a8xkj1aq"))))
+         "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla"))))
     (properties `((upstream-name . "treeio")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e2ec50a93811d09cb3ad468339b44046da2d08ed Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:53 +0200
Subject: gnu: r-ggtree: Update to 3.4.0.

* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index def4da17bc..176de7575b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7010,14 +7010,14 @@ (define-public r-treeio
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "3.2.1")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "0qk39gdpy4kznjhmvi25y2spcdj2r1i6mv673vx8dzf66zfs20v8"))))
+         "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a2cc02fea86ba6e1d3fc839f839023935901bbbf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:53 +0200
Subject: gnu: r-metapod: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-metapod): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 176de7575b..170bdcf251 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7047,14 +7047,14 @@ (define-public r-ggtree
 (define-public r-metapod
   (package
     (name "r-metapod")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "metapod" version))
        (sha256
         (base32
-         "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk"))))
+         "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
     (properties `((upstream-name . "metapod")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 5aad4672519a77a3f7fd97e570ea08ae0d042274 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:53 +0200
Subject: gnu: r-biocsingular: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 170bdcf251..28e18bd45f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7076,14 +7076,14 @@ (define-public r-metapod
 (define-public r-biocsingular
   (package
     (name "r-biocsingular")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSingular" version))
        (sha256
         (base32
-         "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n"))))
+         "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
     (properties `((upstream-name . "BiocSingular")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0258381d438198e1cb009c13ebff4e1ca7bb7757 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:53 +0200
Subject: gnu: r-destiny: Update to 3.10.0.

* gnu/packages/bioconductor.scm (r-destiny): Update to 3.10.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 28e18bd45f..3f45a15216 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7111,14 +7111,14 @@ (define-public r-biocsingular
 (define-public r-destiny
   (package
     (name "r-destiny")
-    (version "3.8.1")
+    (version "3.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "destiny" version))
        (sha256
         (base32
-         "1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc"))))
+         "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
-- 
cgit v1.2.3


From 9641d32660e05a65475ee038804ade23a78786b9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:53 +0200
Subject: gnu: r-savr: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-savr): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3f45a15216..182a9132ee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7155,14 +7155,14 @@ (define-public r-destiny
 (define-public r-savr
   (package
     (name "r-savr")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "savR" version))
        (sha256
         (base32
-         "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky"))))
+         "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
     (properties `((upstream-name . "savR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From f8bab3c5e7be274c0ed00e3d5339c51dd21292a2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:53 +0200
Subject: gnu: r-chipexoqual: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-chipexoqual): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 182a9132ee..1c4b684a38 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7177,14 +7177,14 @@ (define-public r-savr
 (define-public r-chipexoqual
   (package
     (name "r-chipexoqual")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPexoQual" version))
        (sha256
         (base32
-         "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk"))))
+         "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
     (properties `((upstream-name . "ChIPexoQual")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From db8cb101d63e40a04ce4e587b1007d606a7fc779 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:54 +0200
Subject: gnu: r-copynumber: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-copynumber): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1c4b684a38..82df9ac4bf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7217,13 +7217,13 @@ (define-public r-chipexoqual
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.34.0")
+    (version "1.36.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534"))))
+                "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
-- 
cgit v1.2.3


From 9af002ee184e6106103d7561f14030864abcc6ca Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:54 +0200
Subject: gnu: r-dnacopy: Update to 1.70.0.

* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.70.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 82df9ac4bf..c1925cd313 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7237,14 +7237,14 @@ (define-public r-copynumber
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm"))))
+         "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
-- 
cgit v1.2.3


From 3de4ed3fc62fd095b34dd703ae48dc93f674bf38 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:54 +0200
Subject: gnu: r-ebseq: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-ebseq): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c1925cd313..2fe20065f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7335,14 +7335,14 @@ (define-public r-nbpseq
 (define-public r-ebseq
   (package
     (name "r-ebseq")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBSeq" version))
        (sha256
         (base32
-         "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m"))))
+         "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
     (properties `((upstream-name . "EBSeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 266df31f5de9deaf1de6255b8bb4029c319b1fae Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:54 +0200
Subject: gnu: r-karyoploter: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-karyoploter): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2fe20065f1..d517abf5aa 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7357,13 +7357,13 @@ (define-public r-ebseq
 (define-public r-karyoploter
   (package
     (name "r-karyoploter")
-    (version "1.20.3")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "karyoploteR" version))
               (sha256
                (base32
-                "0bcc1ln7602lrbm9wckgyfd9slsqiljjmymj28rfpax1n8rbq44m"))))
+                "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From 5a23854532448a02d705f92884191faf6eee933b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:54 +0200
Subject: gnu: r-lpsymphony: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d517abf5aa..cad35d65fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7395,14 +7395,14 @@ (define-public r-karyoploter
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs"))))
+         "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
     (build-system r-build-system)
     (inputs
      (list zlib))
-- 
cgit v1.2.3


From 00da479a7b497ef56acf6aa32a511884667b09b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:54 +0200
Subject: gnu: r-ihw: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-ihw): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cad35d65fd..fc5d8687ae 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7424,14 +7424,14 @@ (define-public r-lpsymphony
 (define-public r-ihw
   (package
     (name "r-ihw")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IHW" version))
        (sha256
         (base32
-         "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx"))))
+         "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
     (properties `((upstream-name . "IHW")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 76ec28f63b90f504f3da6aa20241a6bd6683ba84 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:55 +0200
Subject: gnu: r-icobra: Update to 1.24.1.

* gnu/packages/bioconductor.scm (r-icobra): Update to 1.24.1.
[propagated-inputs]: Add r-markdown.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fc5d8687ae..07afc46558 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7453,14 +7453,14 @@ (define-public r-ihw
 (define-public r-icobra
   (package
     (name "r-icobra")
-    (version "1.22.2")
+    (version "1.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iCOBRA" version))
        (sha256
         (base32
-         "1ln8l2cp6dqg6zv7s0qnmw5ii93v5sgp0b1nwswl52zdd8mivwxy"))))
+         "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
     (properties `((upstream-name . "iCOBRA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7468,6 +7468,7 @@ (define-public r-icobra
            r-dt
            r-ggplot2
            r-limma
+           r-markdown
            r-reshape2
            r-rocr
            r-scales
-- 
cgit v1.2.3


From 70f5a747786d4ff8dd7470ceb86c048618f4a5c6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:55 +0200
Subject: gnu: r-residualmatrix: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-residualmatrix): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 07afc46558..ddc9b7d2fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7490,14 +7490,14 @@ (define-public r-icobra
 (define-public r-residualmatrix
   (package
     (name "r-residualmatrix")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ResidualMatrix" version))
        (sha256
         (base32
-         "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg"))))
+         "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4"))))
     (properties
      `((upstream-name . "ResidualMatrix")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 2fb6818ab88dc93728ab2eb411ccf43d410d777b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:55 +0200
Subject: gnu: r-mast: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-mast): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ddc9b7d2fd..d60a0d9a7c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7562,14 +7562,14 @@ (define-public r-batchelor
 (define-public r-mast
   (package
     (name "r-mast")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MAST" version))
        (sha256
         (base32
-         "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy"))))
+         "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
     (properties `((upstream-name . "MAST")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 84d78abd525a0fbe2cc88b98f2389d565cd6c265 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:55 +0200
Subject: gnu: r-monocle: Update to 2.24.0.

* gnu/packages/bioconductor.scm (r-monocle): Update to 2.24.0.
[propagated-inputs]: Remove r-densityclust; add r-leidenbase.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d60a0d9a7c..e331dc3326 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7597,14 +7597,14 @@ (define-public r-mast
 (define-public r-monocle
   (package
     (name "r-monocle")
-    (version "2.22.0")
+    (version "2.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "monocle" version))
        (sha256
         (base32
-         "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85"))))
+         "1fyqd7qhij2iyx9vdmgnx2qf0w3kwbkmg805539zrmxry8cwfldb"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
@@ -7613,13 +7613,13 @@ (define-public r-monocle
            r-cluster
            r-combinat
            r-ddrtree
-           r-densityclust
            r-dplyr
            r-fastica
            r-ggplot2
            r-hsmmsinglecell
            r-igraph
            r-irlba
+           r-leidenbase
            r-limma
            r-mass
            r-matrix
-- 
cgit v1.2.3


From 579e05dd9aed907108351ec75875292857f8ce9f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:55 +0200
Subject: gnu: r-noiseq: Update to 2.40.0.

* gnu/packages/bioconductor.scm (r-noiseq): Update to 2.40.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e331dc3326..dee24e34fc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7782,14 +7782,14 @@ (define-public r-monocle3
 (define-public r-noiseq
   (package
     (name "r-noiseq")
-    (version "2.38.0")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "NOISeq" version))
        (sha256
         (base32
-         "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v"))))
+         "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
     (properties `((upstream-name . "NOISeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4221d4588b522fc3eebeff8654021f2c7a5efadb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:55 +0200
Subject: gnu: r-scdd: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-scdd): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dee24e34fc..42c656a893 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7808,14 +7808,14 @@ (define-public r-noiseq
 (define-public r-scdd
   (package
     (name "r-scdd")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scDD" version))
        (sha256
         (base32
-         "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5"))))
+         "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
     (properties `((upstream-name . "scDD")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 52b158dca519b0c884c6ad61b304918d1987724f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:56 +0200
Subject: gnu: r-scone: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-scone): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 42c656a893..101f93decd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7846,14 +7846,14 @@ (define-public r-scdd
 (define-public r-scone
   (package
     (name "r-scone")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scone" version))
        (sha256
         (base32
-         "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1"))))
+         "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aroma-light
-- 
cgit v1.2.3


From 6303dcbc85bd3380f5dafad18b9bb58ea1be1e08 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:56 +0200
Subject: gnu: r-geoquery: Update to 2.64.2.

* gnu/packages/bioconductor.scm (r-geoquery): Update to 2.64.2.
[propagated-inputs]: Remove r-httr; add r-curl.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 101f93decd..5521525f05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7890,21 +7890,21 @@ (define-public r-scone
 (define-public r-geoquery
   (package
     (name "r-geoquery")
-    (version "2.62.2")
+    (version "2.64.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GEOquery" version))
        (sha256
         (base32
-         "1hncr0p54qdg82a771yjjm4w1k2myrc26jzvci3g37mq7bgv3mxw"))))
+         "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
     (properties `((upstream-name . "GEOquery")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
+           r-curl
            r-data-table
            r-dplyr
-           r-httr
            r-limma
            r-magrittr
            r-r-utils
-- 
cgit v1.2.3


From 125c06af915b38be5b544132b46842b439428ea6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:56 +0200
Subject: gnu: r-illuminaio: Update to 0.38.0.

* gnu/packages/bioconductor.scm (r-illuminaio): Update to 0.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5521525f05..0a0b69fc73 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7925,14 +7925,14 @@ (define-public r-geoquery
 (define-public r-illuminaio
   (package
     (name "r-illuminaio")
-    (version "0.36.0")
+    (version "0.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "illuminaio" version))
        (sha256
         (base32
-         "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m"))))
+         "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-base64))
-- 
cgit v1.2.3


From 4ff4b93aa00698069f725b412ba9b0f9ec20b034 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:56 +0200
Subject: gnu: r-siggenes: Update to 1.70.0.

* gnu/packages/bioconductor.scm (r-siggenes): Update to 1.70.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0a0b69fc73..dbaef9d429 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7946,14 +7946,14 @@ (define-public r-illuminaio
 (define-public r-siggenes
   (package
     (name "r-siggenes")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "siggenes" version))
        (sha256
         (base32
-         "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9"))))
+         "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-multtest r-scrime))
-- 
cgit v1.2.3


From 2246d7a2d99bc65e9d5363f3cdb7dce471aca373 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:56 +0200
Subject: gnu: r-bumphunter: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-bumphunter): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dbaef9d429..01c57d5f73 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7970,14 +7970,14 @@ (define-public r-siggenes
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bumphunter" version))
        (sha256
         (base32
-         "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"))))
+         "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From f36df22ceb5357efb07c2b778b10fd98cf8c68ac Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:56 +0200
Subject: gnu: r-minfi: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-minfi): Update to 1.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 01c57d5f73..5cc13c8313 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8004,14 +8004,14 @@ (define-public r-bumphunter
 (define-public r-minfi
   (package
     (name "r-minfi")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minfi" version))
        (sha256
         (base32
-         "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx"))))
+         "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beanplot
-- 
cgit v1.2.3


From a02d652e447c301abf219e5b30ea76e0d50810ea Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:57 +0200
Subject: gnu: r-methylumi: Update to 2.42.0.

* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5cc13c8313..13b480a54c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8055,14 +8055,14 @@ (define-public r-minfi
 (define-public r-methylumi
   (package
     (name "r-methylumi")
-    (version "2.40.1")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "methylumi" version))
        (sha256
         (base32
-         "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka"))))
+         "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotate
-- 
cgit v1.2.3


From 9ccc0373b139a18b0643991ef165498f5b04388c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:57 +0200
Subject: gnu: r-lumi: Update to 2.48.0.

* gnu/packages/bioconductor.scm (r-lumi): Update to 2.48.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 13b480a54c..74ece667b2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8102,14 +8102,14 @@ (define-public r-methylumi
 (define-public r-lumi
   (package
     (name "r-lumi")
-    (version "2.46.0")
+    (version "2.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lumi" version))
        (sha256
         (base32
-         "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in"))))
+         "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
-- 
cgit v1.2.3


From 176a6ccb737e02d398716e0c6f85b19fcccffef5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:57 +0200
Subject: gnu: r-linnorm: Update to 2.20.0.

* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 74ece667b2..d34d91f9e8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8141,14 +8141,14 @@ (define-public r-lumi
 (define-public r-linnorm
   (package
     (name "r-linnorm")
-    (version "2.18.0")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Linnorm" version))
        (sha256
         (base32
-         "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj"))))
+         "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
     (properties `((upstream-name . "Linnorm")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 82ce69aeda22dd9dd6a2e1113334e3df0ad31dd2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:57 +0200
Subject: gnu: r-ioniser: Update to 2.20.0.

* gnu/packages/bioconductor.scm (r-ioniser): Update to 2.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d34d91f9e8..f1583e120a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8202,14 +8202,14 @@ (define-public r-linnorm
 (define-public r-ioniser
   (package
     (name "r-ioniser")
-    (version "2.18.0")
+    (version "2.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "IONiseR" version))
        (sha256
         (base32
-         "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h"))))
+         "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
     (properties `((upstream-name . "IONiseR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0ff26b744a7cb82e097fb7d123d21b7ba0fa9dcc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:57 +0200
Subject: gnu: r-tradeseq: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-tradeseq): Update to 1.10.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f1583e120a..1c2e6747cf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8293,13 +8293,13 @@ (define-public r-metap
 (define-public r-tradeseq
   (package
    (name "r-tradeseq")
-   (version "1.8.0")
+   (version "1.10.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "tradeSeq" version))
             (sha256
              (base32
-              "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j"))))
+              "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biobase
-- 
cgit v1.2.3


From a88487870b4f4e8cdbddab38325885c5bd749198 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:57 +0200
Subject: gnu: r-varianttools: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-varianttools): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1c2e6747cf..11e71d86d5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8362,14 +8362,14 @@ (define-public r-triform
 (define-public r-varianttools
   (package
     (name "r-varianttools")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantTools" version))
        (sha256
         (base32
-         "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl"))))
+         "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
     (properties `((upstream-name . "VariantTools")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c2c13118814fb9271e2c28b4823dbeb0656c166f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:57 +0200
Subject: gnu: r-heatplus: Update to 3.4.0.

* gnu/packages/bioconductor.scm (r-heatplus): Update to 3.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 11e71d86d5..483e8ff41f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8402,14 +8402,14 @@ (define-public r-varianttools
 (define-public r-heatplus
   (package
     (name "r-heatplus")
-    (version "3.2.0")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Heatplus" version))
        (sha256
         (base32
-         "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf"))))
+         "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
     (properties `((upstream-name . "Heatplus")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 50bad20ace5fc5b40175f69def41476387746393 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:58 +0200
Subject: gnu: r-gosemsim: Update to 2.22.0.

* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 483e8ff41f..ad88b14b59 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8427,14 +8427,14 @@ (define-public r-heatplus
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.20.0")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab"))))
+         "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From dde65de5d3400c5f72bc47d3e36d082fcf417c72 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:58 +0200
Subject: gnu: r-anota: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-anota): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ad88b14b59..55c11431a6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8454,14 +8454,14 @@ (define-public r-gosemsim
 (define-public r-anota
   (package
     (name "r-anota")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anota" version))
        (sha256
         (base32
-         "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f"))))
+         "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-multtest r-qvalue))
-- 
cgit v1.2.3


From 9c44834a76e5312bd25938777210cfa1be4011a9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:58 +0200
Subject: gnu: r-sigpathway: Update to 1.64.0.

* gnu/packages/bioconductor.scm (r-sigpathway): Update to 1.64.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55c11431a6..58233fac7b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8484,14 +8484,14 @@ (define-public r-anota
 (define-public r-sigpathway
   (package
     (name "r-sigpathway")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "sigPathway" version))
         (sha256
           (base32
-            "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9"))))
+            "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
     (properties `((upstream-name . "sigPathway")))
     (build-system r-build-system)
     (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
-- 
cgit v1.2.3


From 8b9d7ec80804981a2e3d28ea6b3f0611fe15903a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:58 +0200
Subject: gnu: r-fcscan: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-fcscan): Update to 1.10.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 58233fac7b..5b8ff807a5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8506,13 +8506,13 @@ (define-public r-sigpathway
 (define-public r-fcscan
   (package
     (name "r-fcscan")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fcScan" version))
        (sha256
-        (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd"))))
+        (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
     (properties `((upstream-name . "fcScan")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From cf8935a13073a9556ae332a74538bb1f015fe714 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:58 +0200
Subject: gnu: r-fgsea: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-fgsea): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5b8ff807a5..a0fc9fdef3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8539,14 +8539,14 @@ (define-public r-fcscan
 (define-public r-fgsea
   (package
     (name "r-fgsea")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "fgsea" version))
        (sha256
         (base32
-         "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9"))))
+         "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-bh
-- 
cgit v1.2.3


From 00c890fa471aa0609e70d0ddb5dd9f509c5b5896 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:58 +0200
Subject: gnu: r-dose: Update to 3.22.0.

* gnu/packages/bioconductor.scm (r-dose): Update to 3.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a0fc9fdef3..1aa140748f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8571,14 +8571,14 @@ (define-public r-fgsea
 (define-public r-dose
   (package
     (name "r-dose")
-    (version "3.20.1")
+    (version "3.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DOSE" version))
        (sha256
         (base32
-         "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n"))))
+         "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp"))))
     (properties `((upstream-name . "DOSE")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 7dee98b9aa716885b8afa8a517613299087ca76c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:58 +0200
Subject: gnu: r-enrichplot: Update to 1.16.1.

* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.16.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1aa140748f..0c1dfd5522 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8606,14 +8606,14 @@ (define-public r-dose
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.14.2")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "1rjiqmc32c9gxckgrgbypxpp0m8y0kahvhzvjzymda25xp8zqjs2"))))
+         "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
-- 
cgit v1.2.3


From 54cd450ba8613c46df7e76b3f08c53965e20bd1a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:59 +0200
Subject: gnu: r-clusterprofiler: Update to 4.4.1.

* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.4.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0c1dfd5522..04228c213a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8644,14 +8644,14 @@ (define-public r-enrichplot
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "4.2.2")
+    (version "4.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "1y8ay3fxvcc7a7yqvfc95jfn800ikvs56j17byyp6v08w2j00y76"))))
+         "03bg3agisrm4q10gg57dksvd1ws37if6a1gwcxaybb4c50zadm8p"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From a47875ef726c91ee528a5c57b1e36873e72dab94 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:59 +0200
Subject: gnu: r-clusterexperiment: Update to 2.16.0.

* gnu/packages/bioconductor.scm (r-clusterexperiment): Update to 2.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 04228c213a..2aaf8f5742 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8681,13 +8681,13 @@ (define-public r-clusterprofiler
 (define-public r-clusterexperiment
   (package
     (name "r-clusterexperiment")
-    (version "2.14.0")
+    (version "2.16.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "clusterExperiment" version))
               (sha256
                (base32
-                "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc"))))
+                "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From 479dc1bd20acb341d911ed00f2613467ccfb97cb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:59 +0200
Subject: gnu: r-mlinterfaces: Update to 1.76.0.

* gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.76.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2aaf8f5742..66d341985d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8727,14 +8727,14 @@ (define-public r-clusterexperiment
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
-    (version "1.74.0")
+    (version "1.76.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
-         "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag"))))
+         "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c75a555b5dc87d7dc9620121fb66f8a339622685 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:59 +0200
Subject: gnu: r-annaffy: Update to 1.68.0.

* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.68.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 66d341985d..ed82754469 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8769,14 +8769,14 @@ (define-public r-mlinterfaces
 (define-public r-annaffy
   (package
     (name "r-annaffy")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annaffy" version))
        (sha256
         (base32
-         "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l"))))
+         "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From b80a4781aebf5c1394779ec77d9755caf9224061 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:59 +0200
Subject: gnu: r-a4core: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-a4core): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ed82754469..2292bb6b1c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8801,14 +8801,14 @@ (define-public r-annaffy
 (define-public r-a4core
   (package
     (name "r-a4core")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Core" version))
        (sha256
         (base32
-         "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0"))))
+         "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
     (properties `((upstream-name . "a4Core")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 72a0c0fda2720be87a14934239e749fb1abebb7e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:44:59 +0200
Subject: gnu: r-a4classif: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-a4classif): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2292bb6b1c..6fa4cca6cd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8825,14 +8825,14 @@ (define-public r-a4core
 (define-public r-a4classif
   (package
     (name "r-a4classif")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Classif" version))
        (sha256
         (base32
-         "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb"))))
+         "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
     (properties `((upstream-name . "a4Classif")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 47241c78a0e54b00528959d5c91aecdca8969125 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:00 +0200
Subject: gnu: r-a4preproc: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-a4preproc): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6fa4cca6cd..a357751dca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8855,14 +8855,14 @@ (define-public r-a4classif
 (define-public r-a4preproc
   (package
     (name "r-a4preproc")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Preproc" version))
        (sha256
         (base32
-         "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d"))))
+         "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
     (properties `((upstream-name . "a4Preproc")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 2fa91cea9c85688472ee684dc0f36a6d4ed7cb47 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:00 +0200
Subject: gnu: r-a4reporting: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-a4reporting): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a357751dca..9f6235b7d9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8879,14 +8879,14 @@ (define-public r-a4preproc
 (define-public r-a4reporting
   (package
     (name "r-a4reporting")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Reporting" version))
        (sha256
         (base32
-         "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr"))))
+         "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
     (properties `((upstream-name . "a4Reporting")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c5a596f8b3e649af56f3c0decc980f03d07f915e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:00 +0200
Subject: gnu: r-a4base: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-a4base): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f6235b7d9..a5fb2f3457 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8903,14 +8903,14 @@ (define-public r-a4reporting
 (define-public r-a4base
   (package
     (name "r-a4base")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4Base" version))
        (sha256
         (base32
-         "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy"))))
+         "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
     (properties `((upstream-name . "a4Base")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 73ed8b2361a57c54f2468bb0f235d2042b850008 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:00 +0200
Subject: gnu: r-a4: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-a4): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a5fb2f3457..83d2bca890 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8934,14 +8934,14 @@ (define-public r-a4base
 (define-public r-a4
   (package
     (name "r-a4")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "a4" version))
        (sha256
         (base32
-         "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m"))))
+         "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
-- 
cgit v1.2.3


From 83b5c68b442f8b2300d73c1980b784ecd248950d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:00 +0200
Subject: gnu: r-abseqr: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-abseqr): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 83d2bca890..f549778cdc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8955,14 +8955,14 @@ (define-public r-a4
 (define-public r-abseqr
   (package
     (name "r-abseqr")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "abseqR" version))
        (sha256
         (base32
-         "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz"))))
+         "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From 9dba02ad15280f8544f1a6c193cb082194fd3fd5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:00 +0200
Subject: gnu: r-bacon: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-bacon): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f549778cdc..f3ee55b880 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9003,14 +9003,14 @@ (define-public r-abseqr
 (define-public r-bacon
   (package
     (name "r-bacon")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bacon" version))
        (sha256
         (base32
-         "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"))))
+         "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel r-ellipse r-ggplot2))
-- 
cgit v1.2.3


From bd510b8d7411655642801e3f989700a435963d78 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:00 +0200
Subject: gnu: r-rgadem: Update to 2.44.0.

* gnu/packages/bioconductor.scm (r-rgadem): Update to 2.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f3ee55b880..2f9cc79a53 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9028,14 +9028,14 @@ (define-public r-bacon
 (define-public r-rgadem
   (package
     (name "r-rgadem")
-    (version "2.42.0")
+    (version "2.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
-         "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v"))))
+         "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4"))))
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d124f0fe205de52d116c98452e40f8484e145ea8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:01 +0200
Subject: gnu: r-motifdb: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-motifdb): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2f9cc79a53..1c4d617a42 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9082,12 +9082,12 @@ (define-public r-motiv
 (define-public r-motifdb
   (package
    (name "r-motifdb")
-   (version "1.36.0")
+   (version "1.38.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MotifDb" version))
             (sha256
-             (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425"))))
+             (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
    (properties `((upstream-name . "MotifDb")))
    (build-system r-build-system)
    (propagated-inputs
-- 
cgit v1.2.3


From ef522a58285bd6733278ffd467852f578f2a3aa9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:01 +0200
Subject: gnu: r-motifbreakr: Update to 2.10.0.

* gnu/packages/bioconductor.scm (r-motifbreakr): Update to 2.10.0.
[propagated-inputs]: Remove r-grimport.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1c4d617a42..6e0ed07adf 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9109,12 +9109,12 @@ (define-public r-motifdb
 (define-public r-motifbreakr
   (package
    (name "r-motifbreakr")
-   (version "2.8.0")
+   (version "2.10.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "motifbreakR" version))
             (sha256
-             (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj"))))
+             (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
    (properties `((upstream-name . "motifbreakR")))
    (build-system r-build-system)
    (propagated-inputs
@@ -9124,7 +9124,6 @@ (define-public r-motifbreakr
           r-bsgenome
           r-genomeinfodb
           r-genomicranges
-          r-grimport
           r-gviz
           r-iranges
           r-matrixstats
-- 
cgit v1.2.3


From 81880b4cb7e2214e946cbd6c1d72b4ba49d75aa1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:01 +0200
Subject: gnu: r-motifstack: Update to 1.40.0.

* gnu/packages/bioconductor.scm (r-motifstack): Update to 1.40.0.
[propagated-inputs]: Add r-tfbstools.
---
 gnu/packages/bioconductor.scm | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6e0ed07adf..ebf5696d0b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9159,18 +9159,23 @@ (define-public r-motifbreakr
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz"))))
+         "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml))
+     (list r-ade4
+           r-biostrings
+           r-ggplot2
+           r-htmlwidgets
+           r-tfbstools
+           r-xml))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/motifStack/")
-- 
cgit v1.2.3


From 8f957d34f18d2b7f5213c652f93fc5e110e62439 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:01 +0200
Subject: gnu: r-genomicscores: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ebf5696d0b..d491511a13 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9191,14 +9191,14 @@ (define-public r-motifstack
 (define-public r-genomicscores
   (package
     (name "r-genomicscores")
-    (version "2.6.1")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicScores" version))
        (sha256
         (base32
-         "17v2v7aklljy17nivwmani2jxkbffqs2yr38hlspjlvgpidpf9ln"))))
+         "0zq9k4189dlc14f9rknsc1ffhpjzb2f4fzdaszfdbnd4rr43b79i"))))
     (properties `((upstream-name . "GenomicScores")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 5fce56ab4b61ea6d7dedd1b34180d2d89c3edc19 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:01 +0200
Subject: gnu: r-atacseqqc: Update to 1.20.2.

* gnu/packages/bioconductor.scm (r-atacseqqc): Update to 1.20.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d491511a13..4979948d1a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9228,14 +9228,14 @@ (define-public r-genomicscores
 (define-public r-atacseqqc
   (package
     (name "r-atacseqqc")
-    (version "1.18.1")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ATACseqQC" version))
        (sha256
         (base32
-         "1jmlialnhs9df1hv6l4qk2c4qjyjbz9mdj8vr52ms8vlxlxplz6c"))))
+         "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
     (properties `((upstream-name . "ATACseqQC")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d3ff3a75cd02fa9a5f920a1762410f8c48bc9bf4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:01 +0200
Subject: gnu: r-gofuncr: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-gofuncr): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4979948d1a..c1774a0368 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9275,14 +9275,14 @@ (define-public r-atacseqqc
 (define-public r-gofuncr
   (package
     (name "r-gofuncr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOfuncR" version))
        (sha256
         (base32
-         "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127"))))
+         "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
     (properties `((upstream-name . "GOfuncR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4e95453274b4a926dd5848dea8104dd986f299b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:02 +0200
Subject: gnu: r-annotationtools: Update to 1.70.0.

* gnu/packages/bioconductor.scm (r-annotationtools): Update to 1.70.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c1774a0368..eab102c400 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9380,14 +9380,14 @@ (define-public r-annotationfuncs
 (define-public r-annotationtools
   (package
     (name "r-annotationtools")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotationTools" version))
        (sha256
         (base32
-         "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh"))))
+         "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
     (properties
      `((upstream-name . "annotationTools")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 00eda6acec4237298e8361790eb582d36a805ae2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:02 +0200
Subject: gnu: r-allelicimbalance: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-allelicimbalance): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eab102c400..64107de6d4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9405,14 +9405,14 @@ (define-public r-annotationtools
 (define-public r-allelicimbalance
   (package
     (name "r-allelicimbalance")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AllelicImbalance" version))
        (sha256
         (base32
-         "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq"))))
+         "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
     (properties
      `((upstream-name . "AllelicImbalance")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 5bd8b53432f063e4452c14c8e68c1c084cf5883f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:02 +0200
Subject: gnu: r-aucell: Update to 1.18.1.

* gnu/packages/bioconductor.scm (r-aucell): Update to 1.18.1.
[propagated-inputs]: Remove r-s4vectors; add r-delayedarray and r-delayedmatrixstats.
---
 gnu/packages/bioconductor.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 64107de6d4..c91075198d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9448,23 +9448,24 @@ (define-public r-allelicimbalance
 (define-public r-aucell
   (package
     (name "r-aucell")
-    (version "1.16.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AUCell" version))
        (sha256
         (base32
-         "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp"))))
+         "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
     (properties `((upstream-name . "AUCell")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
            r-data-table
+           r-delayedarray
+           r-delayedmatrixstats
            r-gseabase
            r-mixtools
            r-r-utils
-           r-s4vectors
            r-shiny
            r-summarizedexperiment))
     (native-inputs
-- 
cgit v1.2.3


From f27b8dfc8bced30bd9c8a2460b233a3a1630b674 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:02 +0200
Subject: gnu: r-ebimage: Update to 4.38.0.

* gnu/packages/bioconductor.scm (r-ebimage): Update to 4.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c91075198d..1a48027e29 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9488,14 +9488,14 @@ (define-public r-aucell
 (define-public r-ebimage
   (package
     (name "r-ebimage")
-    (version "4.36.0")
+    (version "4.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBImage" version))
        (sha256
         (base32
-         "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619"))))
+         "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
     (properties `((upstream-name . "EBImage")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From ba6664485619942367ebb13e73c229b59e21a67e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:02 +0200
Subject: gnu: r-yamss: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-yamss): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1a48027e29..0fb6eb2ad4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9527,14 +9527,14 @@ (define-public r-ebimage
 (define-public r-yamss
   (package
     (name "r-yamss")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yamss" version))
        (sha256
         (base32
-         "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab"))))
+         "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
-- 
cgit v1.2.3


From 342986b172ed08b18013ed52c9ff140d9e190261 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:02 +0200
Subject: gnu: r-gtrellis: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fb6eb2ad4..99f566ac08 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9560,14 +9560,14 @@ (define-public r-yamss
 (define-public r-gtrellis
   (package
     (name "r-gtrellis")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gtrellis" version))
        (sha256
         (base32
-         "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl"))))
+         "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-circlize r-genomicranges r-getoptlong r-iranges))
-- 
cgit v1.2.3


From 648b99f7f61153e7d164e674df0576529eb0cf40 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:02 +0200
Subject: gnu: r-somaticsignatures: Update to 2.32.0.

* gnu/packages/bioconductor.scm (r-somaticsignatures): Update to 2.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 99f566ac08..9e6aef4d11 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9586,14 +9586,14 @@ (define-public r-gtrellis
 (define-public r-somaticsignatures
   (package
     (name "r-somaticsignatures")
-    (version "2.30.0")
+    (version "2.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SomaticSignatures" version))
        (sha256
         (base32
-         "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql"))))
+         "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
     (properties
      `((upstream-name . "SomaticSignatures")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From e5694d7e9f95540f279e3e07d9a2c132141576b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:03 +0200
Subject: gnu: r-yapsa: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9e6aef4d11..0580aed291 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9625,14 +9625,14 @@ (define-public r-somaticsignatures
 (define-public r-yapsa
   (package
     (name "r-yapsa")
-    (version "1.20.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "YAPSA" version))
        (sha256
         (base32
-         "08r05fzpraggbxv15lx0b68kjlkysp0rcdlm6n9avzmlsdqplb2h"))))
+         "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
     (properties `((upstream-name . "YAPSA")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3fa5b905620c11acd25bf4c8f9bb3cd095dfdfe2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:03 +0200
Subject: gnu: r-gcrma: Update to 2.68.0.

* gnu/packages/bioconductor.scm (r-gcrma): Update to 2.68.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0580aed291..4ef1c2afb8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9674,14 +9674,14 @@ (define-public r-yapsa
 (define-public r-gcrma
   (package
     (name "r-gcrma")
-    (version "2.66.0")
+    (version "2.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gcrma" version))
        (sha256
         (base32
-         "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001"))))
+         "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-affy
-- 
cgit v1.2.3


From 1ebbd9ee55d8ec24c74c9ce605ec454e8e15d3a5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:03 +0200
Subject: gnu: r-quantro: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-quantro): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4ef1c2afb8..86311bfa6e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9756,14 +9756,14 @@ (define-public r-yaqcaffy
 (define-public r-quantro
   (package
     (name "r-quantro")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "quantro" version))
        (sha256
         (base32
-         "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq"))))
+         "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
-- 
cgit v1.2.3


From 8ae5967136245fcae0c580580daee4ae6356752c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:03 +0200
Subject: gnu: r-yarn: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-yarn): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 86311bfa6e..2f36fd8983 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9789,14 +9789,14 @@ (define-public r-quantro
 (define-public r-yarn
   (package
     (name "r-yarn")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "yarn" version))
        (sha256
         (base32
-         "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d"))))
+         "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
-- 
cgit v1.2.3


From 63035ab55bd1850dcc9678459a84dbf26e52e4b2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:03 +0200
Subject: gnu: r-roar: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-roar): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2f36fd8983..9f3ab5a3bc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9826,14 +9826,14 @@ (define-public r-yarn
 (define-public r-roar
   (package
     (name "r-roar")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "roar" version))
        (sha256
         (base32
-         "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347"))))
+         "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
-- 
cgit v1.2.3


From 9873a3a710aa182c2deaeb06396290d9f678e9c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:04 +0200
Subject: gnu: r-massspecwavelet: Update to 1.62.0.

* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.62.0.
[propagated-inputs]: Remove r-waveslim.
[native-inputs]: Add r-knitr.
---
 gnu/packages/bioconductor.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f3ab5a3bc..2c82898e21 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9894,19 +9894,19 @@ (define-public r-xbseq
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.60.1")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "00irq3i5kfck7rnm8ll7rqhqfpp3bisv2h8is50a7wbd7480z7ij"))))
+         "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
-    (propagated-inputs
-     (list r-waveslim))
+    (native-inputs
+     (list r-knitr))
     (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
     (synopsis "Mass spectrum processing by wavelet-based algorithms")
     (description
-- 
cgit v1.2.3


From d01f1c34241c40b89f3ce78467e432c3eb4c123b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:04 +0200
Subject: gnu: r-xcms: Update to 3.18.0.

* gnu/packages/bioconductor.scm (r-xcms): Update to 3.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2c82898e21..ae5a973921 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9918,14 +9918,14 @@ (define-public r-massspecwavelet
 (define-public r-xcms
   (package
     (name "r-xcms")
-    (version "3.16.1")
+    (version "3.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "xcms" version))
        (sha256
         (base32
-         "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143"))))
+         "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
-- 
cgit v1.2.3


From ec91ec29f1bd44ea65b91a210b873f82b1e22982 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:04 +0200
Subject: gnu: r-wppi: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-wppi): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ae5a973921..b70b008b93 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9959,13 +9959,13 @@ (define-public r-xcms
 (define-public r-wppi
   (package
     (name "r-wppi")
-    (version "1.2.0")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "wppi" version))
               (sha256
                (base32
-                "1spwa8p6w3pyw21dvd1lrhcz1sphdsmsd408jv55ss9nbgvgrp23"))))
+                "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
     (properties `((upstream-name . "wppi")))
     (build-system r-build-system)
     ;; This is necessary because omnipathr attempts to write a configuration
-- 
cgit v1.2.3


From d59260a1dd59789705dac27b61068250bf216f44 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:04 +0200
Subject: gnu: r-wrench: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-wrench): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b70b008b93..7a5887d06e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10000,14 +10000,14 @@ (define-public r-wppi
 (define-public r-wrench
   (package
     (name "r-wrench")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Wrench" version))
        (sha256
         (base32
-         "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n"))))
+         "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
     (properties `((upstream-name . "Wrench")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c0de7bad0a7308e78bcf09708d926e6be2fdecce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:04 +0200
Subject: gnu: r-wiggleplotr: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7a5887d06e..0d7158cbdc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10024,14 +10024,14 @@ (define-public r-wrench
 (define-public r-wiggleplotr
   (package
     (name "r-wiggleplotr")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wiggleplotr" version))
        (sha256
         (base32
-         "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi"))))
+         "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
-- 
cgit v1.2.3


From 30b9b1774b53049428318a422f87e10961e8793b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:04 +0200
Subject: gnu: r-widgettools: Update to 1.74.0.

* gnu/packages/bioconductor.scm (r-widgettools): Update to 1.74.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0d7158cbdc..f2cf3fd8c6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10058,14 +10058,14 @@ (define-public r-wiggleplotr
 (define-public r-widgettools
   (package
     (name "r-widgettools")
-    (version "1.72.0")
+    (version "1.74.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "widgetTools" version))
        (sha256
         (base32
-         "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j"))))
+         "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
     (properties `((upstream-name . "widgetTools")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/widgetTools/")
-- 
cgit v1.2.3


From 6885db9d14e9a6b6dec351da95ae717f25c88168 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:04 +0200
Subject: gnu: r-webbioc: Update to 1.68.0.

* gnu/packages/bioconductor.scm (r-webbioc): Update to 1.68.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f2cf3fd8c6..a94d44f5ad 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10079,14 +10079,14 @@ (define-public r-widgettools
 (define-public r-webbioc
   (package
     (name "r-webbioc")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "webbioc" version))
        (sha256
         (base32
-         "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17"))))
+         "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
     (build-system r-build-system)
     (inputs
      (list netpbm perl))
-- 
cgit v1.2.3


From 40d384423c24f1b08e1d0605e14585aa335c40bf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:05 +0200
Subject: gnu: r-zinbwave: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a94d44f5ad..2a07924261 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10111,14 +10111,14 @@ (define-public r-webbioc
 (define-public r-zinbwave
   (package
     (name "r-zinbwave")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" version))
        (sha256
         (base32
-         "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq"))))
+         "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocparallel
-- 
cgit v1.2.3


From 74abb0cfca6b9cc15e1102ac4e6e09ee28fe37f0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:05 +0200
Subject: gnu: r-zfpkm: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-zfpkm): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2a07924261..a06af1b7d8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10144,14 +10144,14 @@ (define-public r-zinbwave
 (define-public r-zfpkm
   (package
     (name "r-zfpkm")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zFPKM" version))
        (sha256
         (base32
-         "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9"))))
+         "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
     (properties `((upstream-name . "zFPKM")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 7ddf44ccafee26c1484d6f4c10787c23fd0c4aeb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:05 +0200
Subject: gnu: r-rbowtie2: Update to 2.2.0.

* gnu/packages/bioconductor.scm (r-rbowtie2): Update to 2.2.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a06af1b7d8..476dbf332e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10169,14 +10169,14 @@ (define-public r-zfpkm
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x"))))
+         "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From fee94f676b57c4d225c6b39d42737a5d8be10ebb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:05 +0200
Subject: gnu: r-progeny: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-progeny): Update to 1.18.0.
[propagated-inputs]: Add r-decoupler and r-reshape2.
---
 gnu/packages/bioconductor.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 476dbf332e..8991077023 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10196,21 +10196,23 @@ (define-public r-rbowtie2
 (define-public r-progeny
   (package
     (name "r-progeny")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "progeny" version))
        (sha256
         (base32
-         "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y"))))
+         "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
+           r-decoupler
            r-dplyr
            r-ggplot2
            r-ggrepel
            r-gridextra
+           r-reshape2
            r-tidyr))
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From 8fdd1a8aabfbd9171a96156e97337348adc7f133 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:05 +0200
Subject: gnu: r-arrmnormalization: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-arrmnormalization): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8991077023..024c01d28b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10228,14 +10228,14 @@ (define-public r-progeny
 (define-public r-arrmnormalization
   (package
     (name "r-arrmnormalization")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ARRmNormalization" version))
        (sha256
         (base32
-         "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh"))))
+         "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
     (properties
      `((upstream-name . "ARRmNormalization")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 143a3dd032bba6d1f3db353ae52810928340033e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:05 +0200
Subject: gnu: r-biocfilecache: Update to 2.4.0.

* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 024c01d28b..fbce487aad 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10251,14 +10251,14 @@ (define-public r-arrmnormalization
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "2.2.1")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "0gaj0z6dk2p2vhvqz685xwd5q2mkvpimh2493p3w04s2rlsvi3jb"))))
+         "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From bd518b3b8a69c980142f343ee51200b45b882bcc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:06 +0200
Subject: gnu: r-iclusterplus: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fbce487aad..21aa9044e9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10284,14 +10284,14 @@ (define-public r-biocfilecache
 (define-public r-iclusterplus
   (package
     (name "r-iclusterplus")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "iClusterPlus" version))
        (sha256
         (base32
-         "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b"))))
+         "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
     (properties `((upstream-name . "iClusterPlus")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
-- 
cgit v1.2.3


From ac90ccab42e350ffe613c0e0437e83b2eb5f7758 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:06 +0200
Subject: gnu: r-rbowtie: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-rbowtie): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 21aa9044e9..8e7a3e4edc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10314,14 +10314,14 @@ (define-public r-iclusterplus
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr"))))
+         "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (arguments
-- 
cgit v1.2.3


From 5e39a816fe1df2917c3b167f55d2a63ac8931c00 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:06 +0200
Subject: gnu: r-sgseq: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-sgseq): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8e7a3e4edc..49aa230877 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10350,14 +10350,14 @@ (define-public r-rbowtie
 (define-public r-sgseq
   (package
     (name "r-sgseq")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SGSeq" version))
        (sha256
         (base32
-         "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja"))))
+         "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
     (properties `((upstream-name . "SGSeq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 9360c7f1668d25a044275186d4338acc4dca1e26 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:06 +0200
Subject: gnu: r-rhisat2: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-rhisat2): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 49aa230877..b41de4730e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10393,14 +10393,14 @@ (define-public r-sgseq
 (define-public r-rhisat2
   (package
     (name "r-rhisat2")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhisat2" version))
        (sha256
         (base32
-         "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y"))))
+         "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
     (properties `((upstream-name . "Rhisat2")))
     (build-system r-build-system)
     (arguments
-- 
cgit v1.2.3


From 2a5a695855a30ddc621c64554d25a181719c2e4c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:06 +0200
Subject: gnu: r-quasr: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-quasr): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b41de4730e..eebcbe5f5f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10431,14 +10431,14 @@ (define-public r-rhisat2
 (define-public r-quasr
   (package
     (name "r-quasr")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "QuasR" version))
        (sha256
         (base32
-         "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5"))))
+         "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
     (properties `((upstream-name . "QuasR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e037f48fcc30ab0678d6e0f9a186341751c7725d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:06 +0200
Subject: gnu: r-rqc: Update to 1.30.0.

* gnu/packages/bioconductor.scm (r-rqc): Update to 1.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eebcbe5f5f..5de5750d5e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10473,14 +10473,14 @@ (define-public r-quasr
 (define-public r-rqc
   (package
     (name "r-rqc")
-    (version "1.28.0")
+    (version "1.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rqc" version))
        (sha256
         (base32
-         "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071"))))
+         "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
     (properties `((upstream-name . "Rqc")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e5b0fac414fc83ffc8a400448c2490e93da0e0bc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:06 +0200
Subject: gnu: r-birewire: Update to 3.28.0.

* gnu/packages/bioconductor.scm (r-birewire): Update to 3.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5de5750d5e..8ab40d7e1e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10516,14 +10516,14 @@ (define-public r-rqc
 (define-public r-birewire
   (package
     (name "r-birewire")
-    (version "3.26.5")
+    (version "3.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiRewire" version))
        (sha256
         (base32
-         "041i5d08bsc5jqx3309fixjacizs4yi992cwazxghm8mrk3kicbr"))))
+         "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
     (properties `((upstream-name . "BiRewire")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From ea931c7223c266696780ac028bcb4fe2f55057bc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:07 +0200
Subject: gnu: r-multidataset: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-multidataset): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8ab40d7e1e..30dfc9e980 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10569,14 +10569,14 @@ (define-public r-birta
 (define-public r-multidataset
   (package
     (name "r-multidataset")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiDataSet" version))
        (sha256
         (base32
-         "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s"))))
+         "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
     (properties `((upstream-name . "MultiDataSet")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From bc2d0114f8ef7c0df14f78879eab0772bb3d9be5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:07 +0200
Subject: gnu: r-ropls: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-ropls): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 30dfc9e980..f91c7b559f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10606,14 +10606,14 @@ (define-public r-multidataset
 (define-public r-ropls
   (package
     (name "r-ropls")
-    (version "1.26.4")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
-         "19f3wd55860x959h5n7mrivyjdas5b3jmx74lf24xnx23g26f8rn"))))
+         "1i9g32mjknrd2lbz2nisc7nr0gk9byx9aik1i7xdwmq4ndxf8rf7"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-multidataset))
-- 
cgit v1.2.3


From 9986cc0bdfb4b1f8989d537642c333e61539fa7e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:07 +0200
Subject: gnu: r-biosigner: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f91c7b559f..98370a1b4f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10643,14 +10643,14 @@ (define-public r-ropls
 (define-public r-biosigner
   (package
     (name "r-biosigner")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biosigner" version))
        (sha256
         (base32
-         "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"))))
+         "11w28nlz0f06idbna5k9xs891w516401l1zab5gg7s0z3xxaki4f"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls))
-- 
cgit v1.2.3


From eab93418bf72f48f325e88ec36dce2e4db497140 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:07 +0200
Subject: gnu: r-annotatr: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-annotatr): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 98370a1b4f..9de1028086 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10672,14 +10672,14 @@ (define-public r-biosigner
 (define-public r-annotatr
   (package
     (name "r-annotatr")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotatr" version))
        (sha256
         (base32
-         "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i"))))
+         "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From 44b596f088f3d25303a1dae29281ac25287adcea Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:07 +0200
Subject: gnu: r-rsubread: Update to 2.10.1.

* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.10.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9de1028086..bcd357fc85 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10713,14 +10713,14 @@ (define-public r-annotatr
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.8.2")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "078zcchw9xl6vs2wihzzji349vq0m1a039m86jdlvb7nc3i1imfk"))))
+         "1cf80gmzz4c1pvif3350ifsmsbfplyl2na39n8g3x0zkwpl6ijdc"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs (list zlib))
-- 
cgit v1.2.3


From 73b695f06d5ce9f677f62fb7e62991cd2559a556 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:07 +0200
Subject: gnu: r-flowutils: Update to 1.59.0.

* gnu/packages/bioconductor.scm (r-flowutils): Update to 1.59.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bcd357fc85..d0adc8b4f0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10739,14 +10739,14 @@ (define-public r-rsubread
 (define-public r-flowutils
   (package
     (name "r-flowutils")
-    (version "1.58.0")
+    (version "1.59.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowUtils" version))
        (sha256
         (base32
-         "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161"))))
+         "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
     (properties `((upstream-name . "flowUtils")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d44194e8079c0564bca6c609c8990e4c98e45ec3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:08 +0200
Subject: gnu: r-consensusclusterplus: Update to 1.60.0.

* gnu/packages/bioconductor.scm (r-consensusclusterplus): Update to 1.60.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d0adc8b4f0..5fa21f0777 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10765,14 +10765,14 @@ (define-public r-flowutils
 (define-public r-consensusclusterplus
   (package
     (name "r-consensusclusterplus")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ConsensusClusterPlus" version))
        (sha256
         (base32
-         "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr"))))
+         "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
     (properties
      `((upstream-name . "ConsensusClusterPlus")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3f7c9b93a20b1d5340b2866abba0221fbf6b9a1d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:08 +0200
Subject: gnu: r-cytolib: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5fa21f0777..16a0ebca5e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10831,14 +10831,14 @@ (define-public r-cycombine
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.6.2")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "0ycr4wmkfi0rvzwicblkfjgppk72gwwpim0rfiz1s44lycsf4py5"))))
+         "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From e5a261cd3452483a7d4ae2b3a47753a90e22825b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:08 +0200
Subject: gnu: r-flowcore: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-flowcore): Update to 2.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 16a0ebca5e..a7205b2bda 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10860,14 +10860,14 @@ (define-public r-cytolib
 (define-public r-flowcore
   (package
     (name "r-flowcore")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowCore" version))
        (sha256
         (base32
-         "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp"))))
+         "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
     (properties `((upstream-name . "flowCore")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 739beb90c4a47893ba3e7b64a1e0ccdf56efa009 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:08 +0200
Subject: gnu: r-flowmeans: Update to 1.56.0.

* gnu/packages/bioconductor.scm (r-flowmeans): Update to 1.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a7205b2bda..24427e967d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10892,14 +10892,14 @@ (define-public r-flowcore
 (define-public r-flowmeans
   (package
     (name "r-flowmeans")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowMeans" version))
        (sha256
         (base32
-         "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6"))))
+         "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
     (properties `((upstream-name . "flowMeans")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 7db8599d851baef54b87d554c9bd8b22157d7983 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:08 +0200
Subject: gnu: r-ncdfflow: Update to 2.42.0.

* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 24427e967d..b810214fc2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10915,14 +10915,14 @@ (define-public r-flowmeans
 (define-public r-ncdfflow
   (package
     (name "r-ncdfflow")
-    (version "2.40.0")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ncdfFlow" version))
        (sha256
         (base32
-         "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar"))))
+         "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m"))))
     (properties `((upstream-name . "ncdfFlow")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From edbabc91cc0e86e73b6cbb75dc78e4a92cd7981e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:08 +0200
Subject: gnu: r-ggcyto: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b810214fc2..2c8560757b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10946,14 +10946,14 @@ (define-public r-ncdfflow
 (define-public r-ggcyto
   (package
     (name "r-ggcyto")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggcyto" version))
        (sha256
         (base32
-         "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1"))))
+         "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"))))
     (properties `((upstream-name . "ggcyto")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 2c76fce33afb22dd8e621e4f52ee4296b8a30669 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:08 +0200
Subject: gnu: r-flowviz: Update to 1.60.0.

* gnu/packages/bioconductor.scm (r-flowviz): Update to 1.60.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2c8560757b..99321dfb05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10983,14 +10983,14 @@ (define-public r-ggcyto
 (define-public r-flowviz
   (package
     (name "r-flowviz")
-    (version "1.58.0")
+    (version "1.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowViz" version))
        (sha256
         (base32
-         "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04"))))
+         "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f"))))
     (properties `((upstream-name . "flowViz")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 9305453a669876869a2c9de98704ff73df36f245 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:09 +0200
Subject: gnu: r-flowclust: Update to 3.34.0.

* gnu/packages/bioconductor.scm (r-flowclust): Update to 3.34.0.
[propagated-inputs]: Remove r-clue, r-corpcor, r-ellipse, r-flowviz, and r-mnormt.
---
 gnu/packages/bioconductor.scm | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 99321dfb05..2790abd1cd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11014,14 +11014,14 @@ (define-public r-flowviz
 (define-public r-flowclust
   (package
     (name "r-flowclust")
-    (version "3.32.0")
+    (version "3.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowClust" version))
        (sha256
         (base32
-         "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi"))))
+         "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
     (properties `((upstream-name . "flowClust")))
     (build-system r-build-system)
     (arguments
@@ -11030,13 +11030,8 @@ (define-public r-flowclust
     (propagated-inputs
      (list r-biobase
            r-biocgenerics
-           r-clue
-           r-corpcor
-           r-ellipse
            r-flowcore
-           r-flowviz
-           r-graph
-           r-mnormt))
+           r-graph))
     (inputs
      (list gsl))
     (native-inputs
-- 
cgit v1.2.3


From cf72f829dc0eb60d708667483ad00a5b4d1d48c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:09 +0200
Subject: gnu: r-rprotobuflib: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-rprotobuflib): Update to 2.8.0.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2790abd1cd..9471e329e0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11048,14 +11048,14 @@ (define-public r-flowclust
 (define-public r-rprotobuflib
   (package
     (name "r-rprotobuflib")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RProtoBufLib" version))
        (sha256
         (base32
-         "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10"))))
+         "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
     (properties `((upstream-name . "RProtoBufLib")))
     (build-system r-build-system)
     (arguments
@@ -11064,7 +11064,7 @@ (define-public r-rprotobuflib
          (add-after 'unpack 'unpack-bundled-sources
            (lambda _
              (with-directory-excursion "src"
-               (invoke "tar" "xf" "protobuf-3.13.0.tar.gz")))))))
+               (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
     (native-inputs
      (list r-knitr))
     (home-page "https://bioconductor.org/packages/RProtoBufLib/")
-- 
cgit v1.2.3


From 6b078537858891234cb3a2b9ebe515d161006093 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:09 +0200
Subject: gnu: r-flowworkspace: Update to 4.8.0.

* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9471e329e0..f556120ea5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11077,14 +11077,14 @@ (define-public r-rprotobuflib
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
-    (version "4.6.0")
+    (version "4.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
-         "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig"))))
+         "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 1d6586a8c7de69c7afd4b7fd04adeb1754cc29fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:09 +0200
Subject: gnu: r-flowstats: Update to 4.8.0.

* gnu/packages/bioconductor.scm (r-flowstats): Update to 4.8.0.
[propagated-inputs]: Add r-corpcor and r-mnormt.
---
 gnu/packages/bioconductor.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f556120ea5..8b9e3db730 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11131,20 +11131,21 @@ (define-public r-flowworkspace
 (define-public r-flowstats
   (package
     (name "r-flowstats")
-    (version "4.6.0")
+    (version "4.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowStats" version))
        (sha256
         (base32
-         "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9"))))
+         "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj"))))
     (properties `((upstream-name . "flowStats")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biobase
            r-biocgenerics
            r-cluster
+           r-corpcor
            r-fda
            r-flowcore
            r-flowviz
@@ -11153,6 +11154,7 @@ (define-public r-flowstats
            r-ks
            r-lattice
            r-mass
+           r-mnormt
            r-ncdfflow
            r-rcolorbrewer
            r-rrcov))
-- 
cgit v1.2.3


From 31604d4afc28311a40f10043e2f2bb36ff9ee2ec Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:09 +0200
Subject: gnu: r-opencyto: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-opencyto): Update to 2.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8b9e3db730..7b8c4925dc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11169,14 +11169,14 @@ (define-public r-flowstats
 (define-public r-opencyto
   (package
     (name "r-opencyto")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "openCyto" version))
        (sha256
         (base32
-         "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm"))))
+         "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y"))))
     (properties `((upstream-name . "openCyto")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 74abd80a3fa9ad6fa039a5c2c8736402fb899a49 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:09 +0200
Subject: gnu: r-cytoml: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7b8c4925dc..85b4918b06 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11213,14 +11213,14 @@ (define-public r-opencyto
 (define-public r-cytoml
   (package
     (name "r-cytoml")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CytoML" version))
        (sha256
         (base32
-         "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz"))))
+         "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"))))
     (properties `((upstream-name . "CytoML")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From 2b9201ae8a4ebc74841a2dfd8a5cb6158d00bf63 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:10 +0200
Subject: gnu: r-flowsom: Update to 2.4.0.

* gnu/packages/bioconductor.scm (r-flowsom): Update to 2.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 85b4918b06..90bb0f3698 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11265,14 +11265,14 @@ (define-public r-cytoml
 (define-public r-flowsom
   (package
     (name "r-flowsom")
-    (version "2.2.0")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "FlowSOM" version))
        (sha256
         (base32
-         "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f"))))
+         "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
     (properties `((upstream-name . "FlowSOM")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From af575f5b379b1e74bcc574c9f65ed28d5de3ad66 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:10 +0200
Subject: gnu: r-mixomics: Update to 6.20.0.

* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 90bb0f3698..a0aa264540 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11308,14 +11308,14 @@ (define-public r-flowsom
 (define-public r-mixomics
   (package
     (name "r-mixomics")
-    (version "6.18.1")
+    (version "6.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "mixOmics" version))
        (sha256
         (base32
-         "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f"))))
+         "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
     (properties `((upstream-name . "mixOmics")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From b1f4698988f71ba9a07648da2bde79ff133fc406 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:10 +0200
Subject: gnu: r-depecher: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-depecher): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a0aa264540..87cf96d42b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11354,14 +11354,14 @@ (define-public r-mixomics
 (define-public r-depecher
   (package                              ;Source/Weave error
     (name "r-depecher")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DepecheR" version))
        (sha256
         (base32
-         "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9"))))
+         "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
     (properties `((upstream-name . "DepecheR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d88de74e61e28d1abb4e0a4ed9189b84875e95fc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:10 +0200
Subject: gnu: r-rcistarget: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-rcistarget): Update to 1.16.0.
[propagated-inputs]: Remove r-feather; add r-s4vectors.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 87cf96d42b..e4098dc479 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11400,14 +11400,14 @@ (define-public r-depecher
 (define-public r-rcistarget
   (package
     (name "r-rcistarget")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RcisTarget" version))
        (sha256
         (base32
-         "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7"))))
+         "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
     (properties `((upstream-name . "RcisTarget")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11416,11 +11416,11 @@ (define-public r-rcistarget
            r-biocgenerics
            r-data-table
            r-dplyr
-           r-feather
            r-genomeinfodb
            r-genomicranges
            r-gseabase
            r-r-utils
+           r-s4vectors
            r-summarizedexperiment
            r-tibble))
     (native-inputs
-- 
cgit v1.2.3


From 876f7f9c50cb6dbbafcc357939ebce6f5a684acb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:10 +0200
Subject: gnu: r-chicago: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-chicago): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e4098dc479..fd20fbd65e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11442,14 +11442,14 @@ (define-public r-rcistarget
 (define-public r-chicago
   (package
     (name "r-chicago")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Chicago" version))
        (sha256
         (base32
-         "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn"))))
+         "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
     (properties `((upstream-name . "Chicago")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 54e790e6849a4a5e27f87d4728faa6876a99c9b9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:11 +0200
Subject: gnu: r-cicero: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-cicero): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fd20fbd65e..b57824ec98 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11464,14 +11464,14 @@ (define-public r-chicago
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7"))))
+         "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
-- 
cgit v1.2.3


From 840ffa0bfaa45d926f3f272d2cab0156f7e1af4d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:11 +0200
Subject: gnu: r-circrnaprofiler: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.10.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b57824ec98..59c78b7cb2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11531,14 +11531,14 @@ (define-public r-cicero-monocle3
 (define-public r-circrnaprofiler
   (package
     (name "r-circrnaprofiler")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "circRNAprofiler" version))
        (sha256
         (base32
-         "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf"))))
+         "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
     (properties
      `((upstream-name . "circRNAprofiler")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 8ad4197c235bacf188d1b4ce21c8b7ef0559216c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:11 +0200
Subject: gnu: r-genie3: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-genie3): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 59c78b7cb2..1eac98e080 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11666,14 +11666,14 @@ (define-public r-cistopic-next
 (define-public r-genie3
   (package
     (name "r-genie3")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GENIE3" version))
        (sha256
         (base32
-         "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw"))))
+         "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
     (properties `((upstream-name . "GENIE3")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0a649904286665fa02f90ab0251ff305c3601a4d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:11 +0200
Subject: gnu: r-roc: Update to 1.72.0.

* gnu/packages/bioconductor.scm (r-roc): Update to 1.72.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1eac98e080..e49ed9b2c8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11690,14 +11690,14 @@ (define-public r-genie3
 (define-public r-roc
   (package
     (name "r-roc")
-    (version "1.70.0")
+    (version "1.72.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROC" version))
        (sha256
         (base32
-         "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9"))))
+         "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
     (properties `((upstream-name . "ROC")))
     (build-system r-build-system)
     (native-inputs
-- 
cgit v1.2.3


From 0c611d7f4fdbd93ad0cef2ee9f356c8f70ebc4dd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:11 +0200
Subject: gnu: r-watermelon: Update to 2.2.0.

* gnu/packages/bioconductor.scm (r-watermelon): Update to 2.2.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e49ed9b2c8..912b3ed6e9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11712,14 +11712,14 @@ (define-public r-roc
 (define-public r-watermelon
   (package
     (name "r-watermelon")
-    (version "2.0.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wateRmelon" version))
        (sha256
         (base32
-         "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3"))))
+         "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
     (properties `((upstream-name . "wateRmelon")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c9bdb12ba353202a546bd5ff441390cb03f7c540 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:11 +0200
Subject: gnu: r-gdsfmt: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 912b3ed6e9..a36ea34589 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11750,14 +11750,14 @@ (define-public r-watermelon
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp"))
+         "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
-- 
cgit v1.2.3


From c272bc0b1924a936ab36496ad65631b9bf290a8f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:12 +0200
Subject: gnu: r-bigmelon: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a36ea34589..ebc2e97d2a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11806,14 +11806,14 @@ (define-public r-gdsfmt
 (define-public r-bigmelon
   (package
     (name "r-bigmelon")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigmelon" version))
        (sha256
         (base32
-         "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali"))))
+         "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
     (properties `((upstream-name . "bigmelon")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d68798fbd9fc71953cfeb9be60131afbe002c053 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:12 +0200
Subject: gnu: r-seqbias: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-seqbias): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ebc2e97d2a..e48e401ad7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11837,14 +11837,14 @@ (define-public r-bigmelon
 (define-public r-seqbias
   (package
     (name "r-seqbias")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "seqbias" version))
        (sha256
         (base32
-         "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr"))))
+         "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
     (properties `((upstream-name . "seqbias")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 988ed7b0901dcf4ea8743eb7e0f069cbfec3c3e2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:12 +0200
Subject: gnu: r-reqon: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-reqon): Update to 1.42.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e48e401ad7..33df5cbc7b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11861,14 +11861,14 @@ (define-public r-seqbias
 (define-public r-reqon
   (package
     (name "r-reqon")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReQON" version))
        (sha256
         (base32
-         "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1"))))
+         "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
     (properties `((upstream-name . "ReQON")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6291ee1e5b40f22249fa6b9a723aa0ca5943d77b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:12 +0200
Subject: gnu: r-wavcluster: Update to 2.30.0.

* gnu/packages/bioconductor.scm (r-wavcluster): Update to 2.30.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 33df5cbc7b..7de727b69e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11884,14 +11884,14 @@ (define-public r-reqon
 (define-public r-wavcluster
   (package
     (name "r-wavcluster")
-    (version "2.28.0")
+    (version "2.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "wavClusteR" version))
        (sha256
         (base32
-         "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk"))))
+         "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
     (properties `((upstream-name . "wavClusteR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 9825c2b03d3d263229761963b4e53388fb757dd7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:12 +0200
Subject: gnu: r-timeseriesexperiment: Update to 1.13.0.

* gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.13.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7de727b69e..c7d339f011 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11931,14 +11931,14 @@ (define-public r-wavcluster
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
-    (version "1.12.0")
+    (version "1.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TimeSeriesExperiment" version))
        (sha256
         (base32
-         "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d"))))
+         "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
     (properties
      `((upstream-name . "TimeSeriesExperiment")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 286bed66fd9fe5ca59a129a26c8835ab4c0540cd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:12 +0200
Subject: gnu: r-variantfiltering: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-variantfiltering): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c7d339f011..e8978c00ec 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11972,14 +11972,14 @@ (define-public r-timeseriesexperiment
 (define-public r-variantfiltering
   (package
     (name "r-variantfiltering")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "VariantFiltering" version))
        (sha256
         (base32
-         "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p"))))
+         "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
     (properties
      `((upstream-name . "VariantFiltering")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From f27a511f7af5e8b1aa2fa9001538bddd68b946a4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:13 +0200
Subject: gnu: r-variancepartition: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e8978c00ec..4fc7453463 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12078,14 +12078,14 @@ (define-public r-wavetiling
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.24.1")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "14aki7d9xl4rhhzv3cl09mbj1q7xhxg69s4kzms9hfv3cqjryqd7"))))
+         "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From faaa54d0a88f79df01b4234dc47a6715ef2d7b76 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:13 +0200
Subject: gnu: r-htqpcr: Update to 1.50.0.

* gnu/packages/bioconductor.scm (r-htqpcr): Update to 1.50.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4fc7453463..6ff4ef34eb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12126,14 +12126,14 @@ (define-public r-variancepartition
 (define-public r-htqpcr
   (package
     (name "r-htqpcr")
-    (version "1.48.0")
+    (version "1.50.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HTqPCR" version))
        (sha256
         (base32
-         "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3"))))
+         "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
     (properties `((upstream-name . "HTqPCR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6f5cd0539527bd3ef66010e5c8115119441632ef Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:13 +0200
Subject: gnu: r-unifiedwmwqpcr: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6ff4ef34eb..4fec83e68e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12156,14 +12156,14 @@ (define-public r-htqpcr
 (define-public r-unifiedwmwqpcr
   (package
     (name "r-unifiedwmwqpcr")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "unifiedWMWqPCR" version))
        (sha256
         (base32
-         "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk"))))
+         "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
     (properties
      `((upstream-name . "unifiedWMWqPCR")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From fffa2581c35670655f1225969c67f2a6fdc420d8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:13 +0200
Subject: gnu: r-universalmotif: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4fec83e68e..a95a0a8b5e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12180,14 +12180,14 @@ (define-public r-unifiedwmwqpcr
 (define-public r-universalmotif
   (package
     (name "r-universalmotif")
-    (version "1.12.4")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "universalmotif" version))
        (sha256
         (base32
-         "01skcvzd815m3c15ka2pk7z6bggc4l8bhvaf4z9v95i36k4mn5zd"))))
+         "0n2msyyy1xhapkd66j4xwabg4qfd62l01p1nmafjwifnjsx45xvp"))))
     (properties
      `((upstream-name . "universalmotif")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From ac1b83ff821c823445a8f1c752aa30d39b56a2c1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:13 +0200
Subject: gnu: r-ace: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-ace): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a95a0a8b5e..1a7ef1c31b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12228,13 +12228,13 @@ (define-public r-universalmotif
 (define-public r-ace
   (package
     (name "r-ace")
-    (version "1.12.0")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACE" version))
               (sha256
                (base32
-                "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6"))))
+                "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
     (properties `((upstream-name . "ACE")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
-- 
cgit v1.2.3


From 0b03a2f3245711fdafdd3b8a72bd2a1543bb3b1b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:13 +0200
Subject: gnu: r-acgh: Update to 1.74.0.

* gnu/packages/bioconductor.scm (r-acgh): Update to 1.74.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1a7ef1c31b..09e74d2f16 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12257,13 +12257,13 @@ (define-public r-ace
 (define-public r-acgh
   (package
     (name "r-acgh")
-    (version "1.72.0")
+    (version "1.74.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "aCGH" version))
               (sha256
                (base32
-                "1r1q6iq3g7svfn5m4jxlxp413djb40mvf6lh595y86sgwav5k6l4"))))
+                "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
     (properties `((upstream-name . "aCGH")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
-- 
cgit v1.2.3


From 7fd611926e4149510451c42079ace047377a976b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:14 +0200
Subject: gnu: r-acme: Update to 2.52.0.

* gnu/packages/bioconductor.scm (r-acme): Update to 2.52.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 09e74d2f16..9a6c6e0253 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12281,13 +12281,13 @@ (define-public r-acgh
 (define-public r-acme
   (package
     (name "r-acme")
-    (version "2.50.0")
+    (version "2.52.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ACME" version))
               (sha256
                (base32
-                "0h4bqbbqcwc938q7lysk5l35f64xz9d1bsniv2wshmlr4rr0zpcg"))))
+                "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
     (properties `((upstream-name . "ACME")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase r-biocgenerics))
-- 
cgit v1.2.3


From 58386d0f408bd0b335a8f29209fbb6531ba35a53 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:14 +0200
Subject: gnu: r-acde: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-acde): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9a6c6e0253..e70e21c207 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12308,13 +12308,13 @@ (define-public r-acme
 (define-public r-acde
   (package
     (name "r-acde")
-    (version "1.24.0")
+    (version "1.26.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "acde" version))
               (sha256
                (base32
-                "13ks87am73m3bjn9ljapxml2a9cxdpgv9flwvly8aqmi3ndxyqi6"))))
+                "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
     (properties `((upstream-name . "acde")))
     (build-system r-build-system)
     (propagated-inputs (list r-boot))
-- 
cgit v1.2.3


From c988069a9dd8b44aa804a2577f6855585efbe90f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:14 +0200
Subject: gnu: r-bgmix: Update to 1.56.0.

* gnu/packages/bioconductor.scm (r-bgmix): Update to 1.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e70e21c207..a97f89777f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12401,14 +12401,14 @@ (define-public r-activepathways
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn"))))
+         "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8c4e6cfb294dfff6be6178abe380c5c41e50b994 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:14 +0200
Subject: gnu: r-bgx: Update to 1.62.0.

* gnu/packages/bioconductor.scm (r-bgx): Update to 1.62.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a97f89777f..f31d8b22a3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12423,14 +12423,14 @@ (define-public r-bgmix
 (define-public r-bgx
   (package
     (name "r-bgx")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bgx" version))
        (sha256
         (base32
-         "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm"))))
+         "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
     (properties `((upstream-name . "bgx")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3a938a581350cf7ee8b7730d96c44d6bbd1afada Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:14 +0200
Subject: gnu: r-bhc: Update to 1.48.0.

* gnu/packages/bioconductor.scm (r-bhc): Update to 1.48.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f31d8b22a3..9f1e5a388e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12445,14 +12445,14 @@ (define-public r-bgx
 (define-public r-bhc
   (package
     (name "r-bhc")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BHC" version))
        (sha256
         (base32
-         "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2"))))
+         "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
     (properties `((upstream-name . "BHC")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/BHC/")
-- 
cgit v1.2.3


From 0e4dc0e9bfaa58aa602cbc8adaddf382ba9f990b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:14 +0200
Subject: gnu: r-bicare: Update to 1.54.0.

* gnu/packages/bioconductor.scm (r-bicare): Update to 1.54.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f1e5a388e..082a568f85 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12471,14 +12471,14 @@ (define-public r-bhc
 (define-public r-bicare
   (package
     (name "r-bicare")
-    (version "1.52.0")
+    (version "1.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BicARE" version))
        (sha256
         (base32
-         "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6"))))
+         "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
     (properties `((upstream-name . "BicARE")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 5ab4747f7716eafd35f8e163b30e0b20289fdf05 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:14 +0200
Subject: gnu: r-bifet: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-bifet): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 082a568f85..4afce5f7bd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12493,14 +12493,14 @@ (define-public r-bicare
 (define-public r-bifet
   (package
     (name "r-bifet")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiFET" version))
        (sha256
         (base32
-         "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk"))))
+         "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
     (properties `((upstream-name . "BiFET")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 39bd70c43cbe062b49a8b15037d57c9986919801 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:15 +0200
Subject: gnu: r-rsbml: Update to 2.54.0.

* gnu/packages/bioconductor.scm (r-rsbml): Update to 2.54.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4afce5f7bd..c32be2228d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12522,14 +12522,14 @@ (define-public r-bifet
 (define-public r-rsbml
   (package
     (name "r-rsbml")
-    (version "2.52.0")
+    (version "2.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rsbml" version))
        (sha256
         (base32
-         "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2"))))
+         "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
     (properties `((upstream-name . "rsbml")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From 631c408da79b28ae74942d6aa124c977a73de5c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:15 +0200
Subject: gnu: r-hypergraph: Update to 1.68.0.

* gnu/packages/bioconductor.scm (r-hypergraph): Update to 1.68.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c32be2228d..0123994d30 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12548,14 +12548,14 @@ (define-public r-rsbml
 (define-public r-hypergraph
   (package
     (name "r-hypergraph")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hypergraph" version))
        (sha256
         (base32
-         "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf"))))
+         "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
     (properties `((upstream-name . "hypergraph")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a13a4d1e8f71996837e400b9f57d5d23020ab5ee Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:15 +0200
Subject: gnu: r-hyperdraw: Update to 1.48.0.

* gnu/packages/bioconductor.scm (r-hyperdraw): Update to 1.48.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0123994d30..5e8261a420 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12570,14 +12570,14 @@ (define-public r-hypergraph
 (define-public r-hyperdraw
   (package
     (name "r-hyperdraw")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hyperdraw" version))
        (sha256
         (base32
-         "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj"))))
+         "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
     (properties `((upstream-name . "hyperdraw")))
     (build-system r-build-system)
     (inputs (list graphviz))
-- 
cgit v1.2.3


From e273f1ab82e19be5e0ea7bc3eb7bbdf023dcb057 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:15 +0200
Subject: gnu: r-biggr: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-biggr): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5e8261a420..db8cada73a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12592,14 +12592,14 @@ (define-public r-hyperdraw
 (define-public r-biggr
   (package
     (name "r-biggr")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiGGR" version))
        (sha256
         (base32
-         "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr"))))
+         "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
     (properties `((upstream-name . "BiGGR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a2e334d20c4ea394a87b932e26428b2940cd05d9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:15 +0200
Subject: gnu: r-bigpint: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-bigpint): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index db8cada73a..e51911732f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12656,14 +12656,14 @@ (define-public r-bigmemoryextras
 (define-public r-bigpint
   (package
     (name "r-bigpint")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bigPint" version))
        (sha256
         (base32
-         "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q"))))
+         "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
     (properties `((upstream-name . "bigPint")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 985723a862830d9cc76e6b9ca5c0df271144f563 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:15 +0200
Subject: gnu: r-chemminer: Update to 3.48.0.

* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.48.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e51911732f..4c8d83bcae 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12699,14 +12699,14 @@ (define-public r-bigpint
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.46.0")
+    (version "3.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8"))))
+         "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3d99b6af6030bfe72fd203e278061e9d87cdec95 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:16 +0200
Subject: gnu: r-fmcsr: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-fmcsr): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4c8d83bcae..8bf3e1cfa4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12742,13 +12742,13 @@ (define-public r-chemminer
 (define-public r-fmcsr
   (package
     (name "r-fmcsr")
-    (version "1.36.0")
+    (version "1.38.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "fmcsR" version))
         (sha256
-          (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0"))))
+          (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
     (properties `((upstream-name . "fmcsR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4bb7bb8db382fa246efdd0198b653c06a384ed93 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:16 +0200
Subject: gnu: r-bioassayr: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8bf3e1cfa4..24a2e0cbfa 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12771,14 +12771,14 @@ (define-public r-fmcsr
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.32.1")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "0pa8d7p9asp36wddkg779i3b9m12rxik56c54bmclnammr0cz89i"))))
+         "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 63726dee635ac5a98f1529d6953622c02dd9652c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:16 +0200
Subject: gnu: r-biobroom: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-biobroom): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 24a2e0cbfa..24f80a1e18 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12806,14 +12806,14 @@ (define-public r-bioassayr
 (define-public r-biobroom
   (package
     (name "r-biobroom")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobroom" version))
        (sha256
         (base32
-         "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r"))))
+         "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
     (properties `((upstream-name . "biobroom")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8f240ba849787b80c05d7fc47edce5272791b14e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:16 +0200
Subject: gnu: r-graphite: Update to 1.42.0.

* gnu/packages/bioconductor.scm (r-graphite): Update to 1.42.0.
[propagated-inputs]: Remove r-checkmate; add r-rlang.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 24f80a1e18..662d1e8616 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12835,18 +12835,18 @@ (define-public r-biobroom
 (define-public r-graphite
   (package
     (name "r-graphite")
-    (version "1.40.0")
+    (version "1.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "graphite" version))
        (sha256
         (base32
-         "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr"))))
+         "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
     (properties `((upstream-name . "graphite")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs))
+     (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
     (home-page "https://bioconductor.org/packages/graphite/")
     (synopsis "Networks from pathway databases")
     (description
-- 
cgit v1.2.3


From 449b0f0920652c6f7e44241a8c16f2dd753aa96c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:16 +0200
Subject: gnu: r-reactomepa: Update to 1.40.0.

* gnu/packages/bioconductor.scm (r-reactomepa): Update to 1.40.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 662d1e8616..475000aa99 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12858,14 +12858,14 @@ (define-public r-graphite
 (define-public r-reactomepa
   (package
     (name "r-reactomepa")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ReactomePA" version))
        (sha256
         (base32
-         "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b"))))
+         "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
     (properties `((upstream-name . "ReactomePA")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 89c507900714f1b4cb581594e8f411b69d010b59 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:16 +0200
Subject: gnu: r-ebarrays: Update to 2.60.0.

* gnu/packages/bioconductor.scm (r-ebarrays): Update to 2.60.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 475000aa99..50261324f9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12890,14 +12890,14 @@ (define-public r-reactomepa
 (define-public r-ebarrays
   (package
     (name "r-ebarrays")
-    (version "2.58.0")
+    (version "2.60.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "EBarrays" version))
        (sha256
         (base32
-         "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6"))))
+         "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
     (properties `((upstream-name . "EBarrays")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 98074b055352ce048ec3db0ea11c1057cc8b32c8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:17 +0200
Subject: gnu: r-bioccheck: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.32.0.
[propagated-inputs]: Remove r-optparse.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 50261324f9..36273aafb0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12934,13 +12934,13 @@ (define-public r-bioccasestudies
 (define-public r-bioccheck
   (package
     (name "r-bioccheck")
-    (version "1.30.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocCheck" version))
               (sha256
                (base32
-                "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y"))))
+                "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"))))
     (properties
      `((upstream-name . "BiocCheck")))
     (build-system r-build-system)
@@ -12949,7 +12949,6 @@ (define-public r-bioccheck
            r-graph
            r-httr
            r-knitr
-           r-optparse
            r-biocmanager
            r-biocviews
            r-stringdist))
-- 
cgit v1.2.3


From d377dd0e2b21f40bf40cef1955dca8d101a98b1b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:17 +0200
Subject: gnu: r-biocgraph: Update to 1.58.0.

* gnu/packages/bioconductor.scm (r-biocgraph): Update to 1.58.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 36273aafb0..b34ad25f50 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12963,14 +12963,14 @@ (define-public r-bioccheck
 (define-public r-biocgraph
   (package
     (name "r-biocgraph")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocGraph" version))
        (sha256
         (base32
-         "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq"))))
+         "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
     (properties `((upstream-name . "biocGraph")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 52a79b24b6e653e4239c8f7a5dfbc70625c01f6c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:17 +0200
Subject: gnu: r-biocstyle: Update to 2.24.0.

* gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b34ad25f50..d0347b2c8b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12985,13 +12985,13 @@ (define-public r-biocgraph
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.22.0")
+    (version "2.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd"))))
+                "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From ad6185a57cdd6dba0bbceef362ead5d96804331b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:17 +0200
Subject: gnu: r-biocviews: Update to 1.64.0.

* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.64.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d0347b2c8b..da0e758f3c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13009,13 +13009,13 @@ (define-public r-biocstyle
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.62.1")
+    (version "1.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r"))))
+                "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From a2756089efb70180b3b3bf6351705f9a96d8885c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:17 +0200
Subject: gnu: r-experimenthub: Update to 2.4.0.

* gnu/packages/bioconductor.scm (r-experimenthub): Update to 2.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index da0e758f3c..8ecc66d8d0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13037,14 +13037,14 @@ (define-public r-biocviews
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "2.2.1")
+    (version "2.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "0lvd6hyqdfsn5ji714v46qdrb8vr1y38lv0pgw8priab0hpqrbm5"))))
+         "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c3733497e0b61ce13665d56a444cadf555380477 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:18 +0200
Subject: gnu: r-grohmm: Update to 1.30.1.

* gnu/packages/bioconductor.scm (r-grohmm): Update to 1.30.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8ecc66d8d0..6778e70d5a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13071,14 +13071,14 @@ (define-public r-experimenthub
 (define-public r-grohmm
   (package
     (name "r-grohmm")
-    (version "1.28.0")
+    (version "1.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "groHMM" version))
        (sha256
         (base32
-         "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s"))))
+         "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
     (properties `((upstream-name . "groHMM")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4028c2b3b5d2173fda2b1d1f60f0722d7323797b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:18 +0200
Subject: gnu: r-multiassayexperiment: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6778e70d5a..f255cb599b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13098,14 +13098,14 @@ (define-public r-grohmm
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9"))))
+         "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From e833302c582803b25c3ea52ccecc3de48066f89b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:18 +0200
Subject: gnu: r-bioconcotk: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-bioconcotk): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f255cb599b..7105f28b58 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13133,14 +13133,14 @@ (define-public r-multiassayexperiment
 (define-public r-bioconcotk
   (package
     (name "r-bioconcotk")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocOncoTK" version))
        (sha256
         (base32
-         "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9"))))
+         "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
     (properties `((upstream-name . "BiocOncoTK")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From b86b657862e2e3500054ecaefab8ab0d69d98ba1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:18 +0200
Subject: gnu: r-biocor: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-biocor): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7105f28b58..f00eda567b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13178,14 +13178,14 @@ (define-public r-bioconcotk
 (define-public r-biocor
   (package
     (name "r-biocor")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioCor" version))
        (sha256
         (base32
-         "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq"))))
+         "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
     (properties `((upstream-name . "BioCor")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d5875494dd5b466fb0f4e4869f088821d42d2ab4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:18 +0200
Subject: gnu: r-biocpkgtools: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f00eda567b..7b866c7cbd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13205,14 +13205,14 @@ (define-public r-biocor
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.12.2")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "1yz2sgx4xrnw22k3d6q6hkj213bnbb4hbr5ymxnmjnsz551s75ny"))))
+         "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 22300462dd61e452142d673864ab5727c7980766 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:18 +0200
Subject: gnu: r-biocset: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-biocset): Update to 1.10.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7b866c7cbd..e19156e15c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13253,14 +13253,14 @@ (define-public r-biocpkgtools
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "1x5ar9byr85iap2x6y66j31fi17wr31awx1gl3z01sckp0dldx6w"))))
+         "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a56e8ec8fbd02c100f9938dbc604101f79ea3f91 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:19 +0200
Subject: gnu: r-biocworkflowtools: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e19156e15c..4abc46e862 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13291,14 +13291,14 @@ (define-public r-biocset
 (define-public r-biocworkflowtools
   (package
     (name "r-biocworkflowtools")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocWorkflowTools" version))
        (sha256
         (base32
-         "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa"))))
+         "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
     (properties
      `((upstream-name . "BiocWorkflowTools")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 9f3d204c3a5144fcee90b5c98226b68c7b80eabf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:19 +0200
Subject: gnu: r-biodist: Update to 1.68.0.

* gnu/packages/bioconductor.scm (r-biodist): Update to 1.68.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4abc46e862..a7173ae1da 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13324,14 +13324,14 @@ (define-public r-biocworkflowtools
 (define-public r-biodist
   (package
     (name "r-biodist")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioDist" version))
        (sha256
         (base32
-         "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp"))))
+         "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
     (properties `((upstream-name . "bioDist")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0f1295e9e9658db831db34cb24429938bf9a8c0d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:19 +0200
Subject: gnu: r-pcatools: Update to 2.8.0.

* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a7173ae1da..68a4407305 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13346,14 +13346,14 @@ (define-public r-biodist
 (define-public r-pcatools
   (package
     (name "r-pcatools")
-    (version "2.6.0")
+    (version "2.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PCAtools" version))
        (sha256
         (base32
-         "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4"))))
+         "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
     (properties `((upstream-name . "PCAtools")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From dd33e8b062ca71206ee8333b4bb293ae19a75ed2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:19 +0200
Subject: gnu: r-rgreat: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-rgreat): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 68a4407305..4e190805b7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13392,14 +13392,14 @@ (define-public r-pcatools
 (define-public r-rgreat
   (package
     (name "r-rgreat")
-    (version "1.26.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGREAT" version))
        (sha256
         (base32
-         "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl"))))
+         "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
     (properties `((upstream-name . "rGREAT")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3e7b5a45e46d1a0817143d7ba040a6155a7f447a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:19 +0200
Subject: gnu: r-m3c: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-m3c): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4e190805b7..cb87b85358 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13416,14 +13416,14 @@ (define-public r-rgreat
 (define-public r-m3c
   (package
     (name "r-m3c")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "M3C" version))
        (sha256
         (base32
-         "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh"))))
+         "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
     (properties `((upstream-name . "M3C")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0a9838b17d0eeff58f5fcfabc65dae24f19d0c6a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:20 +0200
Subject: gnu: r-icens: Update to 1.68.0.

* gnu/packages/bioconductor.scm (r-icens): Update to 1.68.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cb87b85358..4e5937dee4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13449,14 +13449,14 @@ (define-public r-m3c
 (define-public r-icens
   (package
     (name "r-icens")
-    (version "1.66.0")
+    (version "1.68.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Icens" version))
        (sha256
         (base32
-         "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs"))))
+         "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
     (properties `((upstream-name . "Icens")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 16419c4639c08526fc8699d2f262bc1e1e4c9a70 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:20 +0200
Subject: gnu: r-preprocesscore: Update to 1.58.0.

* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.58.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4e5937dee4..a0e3f2da4b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13572,14 +13572,14 @@ (define-public r-fourcseq
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x"))))
+         "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From c8e364b60901a46d22442fd46c492ad80b6fdf98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:20 +0200
Subject: gnu: r-s4vectors: Update to 0.34.0.

* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a0e3f2da4b..bb8559fb6b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13593,13 +13593,13 @@ (define-public r-preprocesscore
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.32.4")
+    (version "0.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "17dvypxcwp8c7ih23hi2366110by6zq1mjgxkmlbiklzachg9780"))))
+                "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3c57f6d2a0ac98709a06ea5568718c1e60082a0c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:20 +0200
Subject: gnu: r-rgraphviz: Update to 2.40.0.

* gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.40.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bb8559fb6b..aeb1b084f6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13660,14 +13660,14 @@ (define-public r-wgcna
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.38.0")
+    (version "2.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7"))))
+         "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     (arguments
-- 
cgit v1.2.3


From 8b7e1da3b68542d50efb210aadad87acae01bafc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:20 +0200
Subject: gnu: r-fithic: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-fithic): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aeb1b084f6..2f841b3e3e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13698,13 +13698,13 @@ (define-public r-rgraphviz
 (define-public r-fithic
   (package
     (name "r-fithic")
-    (version "1.20.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "FitHiC" version))
               (sha256
                (base32
-                "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y"))))
+                "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
     (properties `((upstream-name . "FitHiC")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 0b0bce35562e70d46740978fb7e09e6cfa0e4653 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:20 +0200
Subject: gnu: r-hitc: Update to 1.40.0.

* gnu/packages/bioconductor.scm (r-hitc): Update to 1.40.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2f841b3e3e..8d203b780c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13722,13 +13722,13 @@ (define-public r-fithic
 (define-public r-hitc
   (package
     (name "r-hitc")
-    (version "1.38.0")
+    (version "1.40.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "HiTC" version))
               (sha256
                (base32
-                "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx"))))
+                "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
     (properties `((upstream-name . "HiTC")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 59519a14deb73c878bfa57c3a59c70f8ef54d714 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:21 +0200
Subject: gnu: r-hdf5array: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8d203b780c..1b9ee8ed2f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13751,14 +13751,14 @@ (define-public r-hitc
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "1al4a88pgdl7hfhphsnwl1gg1c1kmw37wcdr4v4pfsw5l8ff7nx4"))))
+         "0s9vj74359ckmwl8r951jxrzkidslwdl9qamkhz8ilw8b5awxyw4"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3


From 3db60a25a73030fc6bf158fae398d3517888e2ad Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:21 +0200
Subject: gnu: r-rhdf5lib: Update to 1.18.2.

* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.18.2.
[source]: Adjust snippet.
[arguments]: Update build phase 'do-not-use-bundled-hdf5.
---
 gnu/packages/bioconductor.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1b9ee8ed2f..73995c0255 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13782,22 +13782,21 @@ (define-public r-hdf5array
 (define-public r-rhdf5lib
   (package
     (name "r-rhdf5lib")
-    (version "1.16.0")
+    (version "1.18.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhdf5lib" version))
        (sha256
         (base32
-         "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p"))
+         "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            ;; Delete bundled binaries
            (delete-file-recursively "src/wininclude/")
-           (delete-file-recursively "src/winlib-8.3.0/")
-           (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")
-           #t))))
+           (delete-file-recursively "src/winlib/")
+           (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
     (properties `((upstream-name . "Rhdf5lib")))
     (build-system r-build-system)
     (arguments
@@ -13806,11 +13805,8 @@ (define-public r-rhdf5lib
          (add-after 'unpack 'do-not-use-bundled-hdf5
            (lambda* (#:key inputs #:allow-other-keys)
              (for-each delete-file '("configure" "configure.ac"))
-             ;; Do not make other packages link with the proprietary libsz.
              (substitute* "R/zzz.R"
-               ((" \"%s/libsz.a\"") "")
-               (("patharch, .getDynamicLinks")
-                ".getDynamicLinks"))
+               (("return\\(links\\)") "return(\" -lz\")"))
              (with-directory-excursion "src"
                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
                (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
@@ -13829,6 +13825,8 @@ (define-public r-rhdf5lib
                             "hdf5/src/libhdf5.settings")
                (rename-file "Makevars.in" "Makevars")
                (substitute* "Makevars"
+                 (("@BUILD_HDF5@") "")
+                 (("@COPY_SZIP@") "")
                  (("@ZLIB_LIB@") "-lz")
                  (("@ZLIB_INCLUDE@") "")
                  (("HDF5_CXX_LIB=.*")
-- 
cgit v1.2.3


From 18fd5759c70e29789fe8ce88e775f7bee720a740 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:21 +0200
Subject: gnu: r-beachmat: Update to 2.12.0.

* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 73995c0255..b53e8390a2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13862,14 +13862,14 @@ (define-public r-rhdf5lib
 (define-public r-beachmat
   (package
     (name "r-beachmat")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "beachmat" version))
        (sha256
         (base32
-         "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb"))))
+         "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
-- 
cgit v1.2.3


From bde757d11d8e2a302a8bee4b31fdd7138418e7c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:21 +0200
Subject: gnu: r-cner: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-cner): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b53e8390a2..0fe839047d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13888,13 +13888,13 @@ (define-public r-beachmat
 (define-public r-cner
   (package
     (name "r-cner")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CNEr" version))
        (sha256
-        (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2"))))
+        (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
     (properties `((upstream-name . "CNEr")))
     (build-system r-build-system)
     (inputs (list zlib))
-- 
cgit v1.2.3


From 7c9793b3e8ef654538e8b0b49549c8afdd131cf2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:21 +0200
Subject: gnu: r-tfbstools: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-tfbstools): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fe839047d..a8a673cf4c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13936,14 +13936,14 @@ (define-public r-cner
 (define-public r-tfbstools
   (package
     (name "r-tfbstools")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TFBSTools" version))
        (sha256
         (base32
-         "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g"))))
+         "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
     (properties `((upstream-name . "TFBSTools")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e213375069ef72aab745183e9760c5fb68e35c92 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:21 +0200
Subject: gnu: r-maftools: Update to 2.12.0.

* gnu/packages/bioconductor.scm (r-maftools): Update to 2.12.0.
[propagated-inputs]: Add r-dnacopy.
---
 gnu/packages/bioconductor.scm | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a8a673cf4c..feda9ccc1f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13982,17 +13982,22 @@ (define-public r-tfbstools
 (define-public r-maftools
   (package
     (name "r-maftools")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "maftools" version))
        (sha256
-        (base32 "1s8w3xwwigz803l81bs9cb2dbvvw5r9z8jjcav1rmh9wm8909nfd"))))
+        (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
     (properties `((upstream-name . "maftools")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-data-table r-rcolorbrewer r-rhtslib r-survival r-zlibbioc))
+     (list r-data-table
+           r-dnacopy
+           r-rcolorbrewer
+           r-rhtslib
+           r-survival
+           r-zlibbioc))
     (native-inputs (list r-knitr))
     (home-page "https://github.com/PoisonAlien/maftools")
     (synopsis "Summarize, analyze and visualize MAF files")
-- 
cgit v1.2.3


From 3ef47df3b611062574f950fb8a777adecabe5618 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:22 +0200
Subject: gnu: r-motifmatchr: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-motifmatchr): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index feda9ccc1f..db4417bbee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14011,14 +14011,14 @@ (define-public r-maftools
 (define-public r-motifmatchr
   (package
     (name "r-motifmatchr")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifmatchr" version))
        (sha256
         (base32
-         "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z"))))
+         "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
     (properties `((upstream-name . "motifmatchr")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d9d9f78391009b122662db1ed279dff3e36aff28 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:22 +0200
Subject: gnu: r-chromvar: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-chromvar): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index db4417bbee..e9157793ef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14045,13 +14045,13 @@ (define-public r-motifmatchr
 (define-public r-chromvar
   (package
     (name "r-chromvar")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromVAR" version))
        (sha256
-        (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk"))))
+        (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
     (properties `((upstream-name . "chromVAR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From decd8480f6d86931c1f9918131604c5ccc1d98e5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:22 +0200
Subject: gnu: r-singlecellexperiment: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e9157793ef..25857f93dd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14092,14 +14092,14 @@ (define-public r-chromvar
 (define-public r-singlecellexperiment
   (package
     (name "r-singlecellexperiment")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleCellExperiment" version))
        (sha256
         (base32
-         "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39"))))
+         "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
     (properties
      `((upstream-name . "SingleCellExperiment")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 816a1ba4dc7bff61b22634c2dbcede300070ae3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:22 +0200
Subject: gnu: r-singler: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-singler): Update to 1.10.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 25857f93dd..2905b0398d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14120,13 +14120,13 @@ (define-public r-singlecellexperiment
 (define-public r-singler
   (package
     (name "r-singler")
-    (version "1.8.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SingleR" version))
        (sha256
-        (base32 "0j0h6ipm65wv38qx40z16h01mfirpshfn4lhlwlg2nri4vmihlpi"))))
+        (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
     (properties `((upstream-name . "SingleR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a8fbcbdb7aa17f7c0d72e2f896ae594bba555a17 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:22 +0200
Subject: gnu: r-scuttle: Update to 1.6.2.

* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.6.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2905b0398d..244cb1b9e6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14152,14 +14152,14 @@ (define-public r-singler
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.4.0")
+    (version "1.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467"))))
+         "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 9631f2190aac830bf27322e5d3c7eff7e2153099 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:22 +0200
Subject: gnu: r-scater: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-scater): Update to 1.24.0.
[propagated-inputs]: Add r-rcppml.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 244cb1b9e6..cc1469e24b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14187,13 +14187,13 @@ (define-public r-scuttle
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.22.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg"))))
+                "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
@@ -14209,6 +14209,7 @@ (define-public r-scater
            r-gridextra
            r-matrix
            r-rcolorbrewer
+           r-rcppml
            r-rlang
            r-rtsne
            r-s4vectors
-- 
cgit v1.2.3


From 5f04cf7bdb81d1878b0ba621922250de7e595e6d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:23 +0200
Subject: gnu: r-scran: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-scran): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cc1469e24b..d0e15d26cc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14229,14 +14229,14 @@ (define-public r-scater
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.22.1")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic"))))
+         "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
-- 
cgit v1.2.3


From eca29a788b141c35be821d6ef290fe17c611050e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:23 +0200
Subject: gnu: r-sparsematrixstats: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d0e15d26cc..0490e63007 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14272,14 +14272,14 @@ (define-public r-scran
 (define-public r-sparsematrixstats
   (package
     (name "r-sparsematrixstats")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "sparseMatrixStats" version))
        (sha256
         (base32
-         "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1"))))
+         "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
     (properties
      `((upstream-name . "sparseMatrixStats")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 9381702bbc619756599c084578fcdf391b6c1b79 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:23 +0200
Subject: gnu: r-delayedmatrixstats: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.18.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0490e63007..b4018b6b83 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14297,14 +14297,14 @@ (define-public r-sparsematrixstats
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.16.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk"))))
+         "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From ec7849c360479ab6818d99ce753e523ff10cf927 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:23 +0200
Subject: gnu: r-mscoreutils: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b4018b6b83..af8f4332c0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14333,14 +14333,14 @@ (define-public r-delayedmatrixstats
 (define-public r-mscoreutils
   (package
     (name "r-mscoreutils")
-    (version "1.6.2")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsCoreUtils" version))
        (sha256
         (base32
-         "0614a830gf676ck8j5lkm04158pfvhjb61p3xfdd69gg3d44mk1d"))))
+         "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
     (properties `((upstream-name . "MsCoreUtils")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d34a40c4c03e34a2cfc8514cd217e0b10e09665e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:23 +0200
Subject: gnu: r-msfeatures: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-msfeatures): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index af8f4332c0..70ecf15e23 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14362,13 +14362,13 @@ (define-public r-mscoreutils
 (define-public r-msfeatures
   (package
     (name "r-msfeatures")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MsFeatures" version))
        (sha256
-        (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq"))))
+        (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
     (properties `((upstream-name . "MsFeatures")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From f185bf805c22d08e6bdd9f8bb1b1def85a263a5c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:23 +0200
Subject: gnu: r-biocio: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-biocio): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 70ecf15e23..2d8a470f03 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14392,14 +14392,14 @@ (define-public r-msfeatures
 (define-public r-biocio
   (package
     (name "r-biocio")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "BiocIO" version))
         (sha256
           (base32
-            "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr"))))
+            "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
     (properties `((upstream-name . "BiocIO")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d99da8bb1c289863d979640e4970f002d8683d43 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:24 +0200
Subject: gnu: r-msmseda: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-msmseda): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2d8a470f03..107715aa32 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14425,14 +14425,14 @@ (define-public r-biocio
 (define-public r-msmseda
   (package
     (name "r-msmseda")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsEDA" version))
        (sha256
         (base32
-         "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9"))))
+         "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
     (properties `((upstream-name . "msmsEDA")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e4a8e6dab4acb2741fd275a54a022c9761b2abaf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:24 +0200
Subject: gnu: r-msmstests: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-msmstests): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 107715aa32..255b8c39aa 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14448,14 +14448,14 @@ (define-public r-msmseda
 (define-public r-msmstests
   (package
     (name "r-msmstests")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "msmsTests" version))
        (sha256
         (base32
-         "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb"))))
+         "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
     (properties `((upstream-name . "msmsTests")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 1b75b53a0e0c60afabdf7f25b403a819261ad1bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:24 +0200
Subject: gnu: r-catalyst: Update to 1.20.1.

* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.20.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 255b8c39aa..65453b78b3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14477,14 +14477,14 @@ (define-public r-msmstests
 (define-public r-catalyst
   (package
     (name "r-catalyst")
-    (version "1.18.1")
+    (version "1.20.1")
     (source
       (origin
         (method url-fetch)
         (uri (bioconductor-uri "CATALYST" version))
         (sha256
           (base32
-            "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0"))))
+            "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
     (properties `((upstream-name . "CATALYST")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 534743333e0a9c9e9a3d7aa2d01f76814ca0ae39 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:24 +0200
Subject: gnu: r-erma: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-erma): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 65453b78b3..51c97e5d50 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14540,14 +14540,14 @@ (define-public r-catalyst
 (define-public r-erma
   (package
     (name "r-erma")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "erma" version))
        (sha256
         (base32
-         "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z"))))
+         "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From 97ea85bfcff36f790b8cb07dba243e36e3d3db43 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:24 +0200
Subject: gnu: r-ggbio: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-ggbio): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 51c97e5d50..07a3692600 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14580,14 +14580,14 @@ (define-public r-erma
 (define-public r-ggbio
   (package
     (name "r-ggbio")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggbio" version))
        (sha256
         (base32
-         "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7"))))
+         "1lvms07ba99nzf10gpn50wjca84nj5jrb6902z069p2bfi4xyd27"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From b6f77fdc872d6d9dec27fe99cc14f66a3e6e9e74 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:25 +0200
Subject: gnu: r-gviz: Update to 1.40.1.

* gnu/packages/bioconductor.scm (r-gviz): Update to 1.40.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 07a3692600..b1ceff5ad8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14748,14 +14748,14 @@ (define-public r-gqtlstats
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.38.4")
+    (version "1.40.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "14qybi5b3h9z5b0m127jf7z695amf612rh5wq2g2n1yirfhzbdja"))))
+         "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From ee71b376ecfadb220066d24acebff0a4d1665543 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:25 +0200
Subject: gnu: r-gwascat: Update to 2.28.1.

* gnu/packages/bioconductor.scm (r-gwascat): Update to 2.28.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b1ceff5ad8..0c1ffcf161 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14797,14 +14797,14 @@ (define-public r-gviz
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.26.0")
+    (version "2.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx"))))
+         "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
-- 
cgit v1.2.3


From 564024c01f6461f3249e4811cff3a0980cdb7e87 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:25 +0200
Subject: gnu: r-kegggraph: Update to 1.56.0.

* gnu/packages/bioconductor.scm (r-kegggraph): Update to 1.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0c1ffcf161..73478299c5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14831,13 +14831,13 @@ (define-public r-gwascat
 (define-public r-kegggraph
   (package
     (name "r-kegggraph")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGgraph" version))
        (sha256
-        (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4"))))
+        (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
     (properties `((upstream-name . "KEGGgraph")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c8f930d575792b16cafa7ae6b08d461308f092a8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:25 +0200
Subject: gnu: r-ldblock: Update to 1.26.0.

* gnu/packages/bioconductor.scm (r-ldblock): Update to 1.26.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 73478299c5..6aaac8c0c4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14855,14 +14855,14 @@ (define-public r-kegggraph
 (define-public r-ldblock
   (package
     (name "r-ldblock")
-    (version "1.24.0")
+    (version "1.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ldblock" version))
        (sha256
         (base32
-         "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg"))))
+         "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biocgenerics
-- 
cgit v1.2.3


From c784304f9ba451c18631b22a08381bfc45371642 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:25 +0200
Subject: gnu: r-pathview: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-pathview): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6aaac8c0c4..f4c8cdadc7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14979,13 +14979,13 @@ (define-public r-spp
 (define-public r-pathview
   (package
     (name "r-pathview")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "pathview" version))
        (sha256
-        (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr"))))
+        (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"))))
     (properties `((upstream-name . "pathview")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 93b59aca4c3c11b62af38cb306259be73f828cba Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:25 +0200
Subject: gnu: r-snpstats: Update to 1.46.0.

* gnu/packages/bioconductor.scm (r-snpstats): Update to 1.46.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f4c8cdadc7..592af1b0d9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15013,14 +15013,14 @@ (define-public r-pathview
 (define-public r-snpstats
   (package
     (name "r-snpstats")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "snpStats" version))
        (sha256
         (base32
-         "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq"))))
+         "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
     (properties `((upstream-name . "snpStats")))
     (build-system r-build-system)
     (inputs (list zlib))
-- 
cgit v1.2.3


From 80f63620c5bd9b64a4ccca3921de36330580c35e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:26 +0200
Subject: gnu: r-chromstar: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-chromstar): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 592af1b0d9..f863adc249 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15037,14 +15037,14 @@ (define-public r-snpstats
 (define-public r-chromstar
   (package
     (name "r-chromstar")
-    (version "1.20.2")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaR" version))
        (sha256
         (base32
-         "1akcmxzn4j9ph4n3lsgfh8fh8hrb28jjamz037w59bsdkcv6wyjq"))))
+         "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
     (properties `((upstream-name . "chromstaR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8467426bba938c12a966a943e5904f5751cbf14c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:26 +0200
Subject: gnu: r-guitar: Update to 2.12.0.

* gnu/packages/bioconductor.scm (r-guitar): Update to 2.12.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f863adc249..b63ebd8b95 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15075,14 +15075,14 @@ (define-public r-chromstar
 (define-public r-guitar
   (package
     (name "r-guitar")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Guitar" version))
        (sha256
         (base32
-         "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9"))))
+         "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
     (properties `((upstream-name . "Guitar")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From d57d65a6284ed917437bc2d17cb89099473eb2cf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:26 +0200
Subject: gnu: r-sushi: Update to 1.34.0.

* gnu/packages/bioconductor.scm (r-sushi): Update to 1.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b63ebd8b95..63c273d529 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15107,13 +15107,13 @@ (define-public r-guitar
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.32.0")
+    (version "1.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "073mh1d063ph5zk1d8kipgblr4l1ixqbxflhq4669761fi2frlw4"))))
+                "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c2a8c4c248441b37683c9e7ebf97f01cab381f95 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:26 +0200
Subject: gnu: r-ballgown: Update to 2.28.0.

* gnu/packages/bioconductor.scm (r-ballgown): Update to 2.28.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 63c273d529..691f9a95b7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15128,14 +15128,14 @@ (define-public r-sushi
 (define-public r-ballgown
   (package
     (name "r-ballgown")
-    (version "2.26.0")
+    (version "2.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ballgown" version))
        (sha256
         (base32
-         "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf"))))
+         "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
     (properties `((upstream-name . "ballgown")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 64c3498d9fe6a99f5fb785ef39d66ae760627300 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:26 +0200
Subject: gnu: r-megadepth: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-megadepth): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 691f9a95b7..ec2d5488b3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15162,14 +15162,14 @@ (define-public r-ballgown
 (define-public r-megadepth
   (package
     (name "r-megadepth")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "megadepth" version))
        (sha256
         (base32
-         "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"))))
+         "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
     (properties `((upstream-name . "megadepth")))
     (build-system r-build-system)
     (inputs (list megadepth))
-- 
cgit v1.2.3


From 460680ef90cfe3c8f4d95b7bf3108111ca2af08f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:26 +0200
Subject: gnu: r-beclear: Update to 2.12.0.

* gnu/packages/bioconductor.scm (r-beclear): Update to 2.12.0.
[propagated-inputs]: Remove r-outliers; add r-dixontest.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ec2d5488b3..cd41cc5f10 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15195,23 +15195,23 @@ (define-public r-megadepth
 (define-public r-beclear
   (package
     (name "r-beclear")
-    (version "2.10.0")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BEclear" version))
        (sha256
         (base32
-         "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29"))))
+         "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
     (properties `((upstream-name . "BEclear")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-abind
            r-biocparallel
            r-data-table
+           r-dixontest
            r-futile-logger
            r-matrix
-           r-outliers
            r-rcpp
            r-rdpack))
     (native-inputs
-- 
cgit v1.2.3


From 00025cdd230569993c72322f27809191fe2dbf8c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:27 +0200
Subject: gnu: r-bgeecall: Update to 1.12.1.

* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.12.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index cd41cc5f10..010b762861 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15228,14 +15228,14 @@ (define-public r-beclear
 (define-public r-bgeecall
   (package
     (name "r-bgeecall")
-    (version "1.10.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeCall" version))
        (sha256
         (base32
-         "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16"))))
+         "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"))))
     (properties `((upstream-name . "BgeeCall")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 24c13f9d64c336ec0a611ca3cac35a7f70eb8b9c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:27 +0200
Subject: gnu: r-bgeedb: Update to 2.22.0.

* gnu/packages/bioconductor.scm (r-bgeedb): Update to 2.22.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 010b762861..bd476a2bb7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15264,14 +15264,14 @@ (define-public r-bgeecall
 (define-public r-bgeedb
   (package
     (name "r-bgeedb")
-    (version "2.20.1")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BgeeDB" version))
        (sha256
         (base32
-         "0mrw7fwjx8k0a5c3iw2j94h1yn5pkvqil7fbzih9xiafnpbn374m"))))
+         "093zk43x8i9ajaqsdhndkyal3dizllr3g85ziavb3k73dzvarzsc"))))
     (properties `((upstream-name . "BgeeDB")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 395f152b926932a81cf151f34fea0502738afe98 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:45:27 +0200
Subject: gnu: r-biobtreer: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-biobtreer): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bd476a2bb7..db192834aa 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15298,14 +15298,14 @@ (define-public r-bgeedb
 (define-public r-biobtreer
   (package
     (name "r-biobtreer")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biobtreeR" version))
        (sha256
         (base32
-         "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s"))))
+         "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
     (properties `((upstream-name . "biobtreeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c4f8b5759a7f9c45282236793d1c86a7c2eb2e5d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:47 +0200
Subject: gnu: r-minet: Update to 3.54.0.

* gnu/packages/bioconductor.scm (r-minet): Update to 3.54.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index db192834aa..ccec896ae3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15322,14 +15322,14 @@ (define-public r-biobtreer
 (define-public r-minet
   (package
     (name "r-minet")
-    (version "3.52.0")
+    (version "3.54.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "minet" version))
        (sha256
         (base32
-         "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd"))))
+         "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
     (properties `((upstream-name . "minet")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3c65a7d577f473144e0b483d63514863690fe0ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:47 +0200
Subject: gnu: r-genetclassifier: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-genetclassifier): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ccec896ae3..b7c41d0f1d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15344,14 +15344,14 @@ (define-public r-minet
 (define-public r-genetclassifier
   (package
     (name "r-genetclassifier")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geNetClassifier" version))
        (sha256
         (base32
-         "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km"))))
+         "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
     (properties
      `((upstream-name . "geNetClassifier")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 5d2c07021cd120215bd3136e0e2ed0f899659516 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:47 +0200
Subject: gnu: r-dir-expiry: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-dir-expiry): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b7c41d0f1d..d3e8b77edc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15369,14 +15369,14 @@ (define-public r-genetclassifier
 (define-public r-dir-expiry
   (package
     (name "r-dir-expiry")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dir.expiry" version))
        (sha256
         (base32
-         "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00"))))
+         "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
     (properties `((upstream-name . "dir.expiry")))
     (build-system r-build-system)
     (propagated-inputs (list r-filelock))
-- 
cgit v1.2.3


From 90e56ba6e3ba7909863236e0976901d152303b20 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:47 +0200
Subject: gnu: r-basilisk-utils: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-basilisk-utils): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d3e8b77edc..238c01a51f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15393,14 +15393,14 @@ (define-public r-dir-expiry
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk.utils" version))
        (sha256
         (base32
-         "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99"))))
+         "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
     (properties
      `((upstream-name . "basilisk.utils")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From b007802e4bbe89c305aa2b6f457d4d2e0907187e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:47 +0200
Subject: gnu: r-basilisk: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-basilisk): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 238c01a51f..b17ac0e9d5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15417,14 +15417,14 @@ (define-public r-basilisk-utils
 (define-public r-basilisk
   (package
     (name "r-basilisk")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "basilisk" version))
        (sha256
         (base32
-         "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a"))))
+         "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"))))
     (properties `((upstream-name . "basilisk")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6766fbb003995adf12a13ecd0e9ac96186e34937 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:47 +0200
Subject: gnu: r-biocthis: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-biocthis): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b17ac0e9d5..f0e5760412 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15443,14 +15443,14 @@ (define-public r-basilisk
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biocthis" version))
        (sha256
         (base32
-         "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39"))))
+         "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
     (properties `((upstream-name . "biocthis")))
     (build-system r-build-system)
     (arguments
-- 
cgit v1.2.3


From 259c003f026b82768c8d4b5c2e82ae97eb8fee79 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:48 +0200
Subject: gnu: r-biocdockermanager: Update to 1.8.0.

* gnu/packages/bioconductor.scm (r-biocdockermanager): Update to 1.8.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f0e5760412..1900ee217c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15477,14 +15477,14 @@ (define-public r-biocthis
 (define-public r-biocdockermanager
   (package
     (name "r-biocdockermanager")
-    (version "1.6.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocDockerManager" version))
        (sha256
         (base32
-         "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w"))))
+         "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"))))
     (properties
      `((upstream-name . "BiocDockerManager")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 12ee563b41466cae1609790e5712dd1209ab4948 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:48 +0200
Subject: gnu: r-biodb: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-biodb): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1900ee217c..0e3c8b85ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15507,14 +15507,14 @@ (define-public r-biocdockermanager
 (define-public r-biodb
   (package
     (name "r-biodb")
-    (version "1.2.2")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biodb" version))
        (sha256
         (base32
-         "0b5zva16r4kz8736h3djjgmh35nxmlin4f374rb4i2s55zsrb638"))))
+         "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"))))
     (properties `((upstream-name . "biodb")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From eb18527e5ff5dad0cf90f005309829caecb213ac Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:48 +0200
Subject: gnu: r-biomformat: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-biomformat): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0e3c8b85ca..5a0145898d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15552,14 +15552,14 @@ (define-public r-biodb
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817"))))
+         "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From a3a8109fe854fcfd6202ccf3327ef87d00222adc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:48 +0200
Subject: gnu: r-mvcclass: Update to 1.70.0.

* gnu/packages/bioconductor.scm (r-mvcclass): Update to 1.70.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5a0145898d..59e70896f3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15581,14 +15581,14 @@ (define-public r-biomformat
 (define-public r-mvcclass
   (package
     (name "r-mvcclass")
-    (version "1.68.0")
+    (version "1.70.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MVCClass" version))
        (sha256
         (base32
-         "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z"))))
+         "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
     (properties `((upstream-name . "MVCClass")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/MVCClass")
-- 
cgit v1.2.3


From 7fe83026b7491108c6bbfd76a13b0c8cb57d2406 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:48 +0200
Subject: gnu: r-biomvcclass: Update to 1.64.0.

* gnu/packages/bioconductor.scm (r-biomvcclass): Update to 1.64.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 59e70896f3..a3f283f18d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15601,14 +15601,14 @@ (define-public r-mvcclass
 (define-public r-biomvcclass
   (package
     (name "r-biomvcclass")
-    (version "1.62.0")
+    (version "1.64.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioMVCClass" version))
        (sha256
         (base32
-         "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j"))))
+         "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
     (properties `((upstream-name . "BioMVCClass")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 3391ff6ddb813ddc7865a36a691bd0fbadea58c7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:48 +0200
Subject: gnu: r-biomvrcns: Update to 1.36.0.

* gnu/packages/bioconductor.scm (r-biomvrcns): Update to 1.36.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a3f283f18d..0ddbdc2f78 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15623,14 +15623,14 @@ (define-public r-biomvcclass
 (define-public r-biomvrcns
   (package
     (name "r-biomvrcns")
-    (version "1.34.0")
+    (version "1.36.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomvRCNS" version))
        (sha256
         (base32
-         "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy"))))
+         "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
     (properties `((upstream-name . "biomvRCNS")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From f5262fa4edf71742fdf93d142b6fd89a5b3a2fc2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:49 +0200
Subject: gnu: r-bionero: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-bionero): Update to 1.4.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0ddbdc2f78..3e80b2ab8b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15648,14 +15648,14 @@ (define-public r-biomvrcns
 (define-public r-bionero
   (package
     (name "r-bionero")
-    (version "1.2.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNERO" version))
        (sha256
         (base32
-         "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p"))))
+         "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"))))
     (properties `((upstream-name . "BioNERO")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 8fe9bcf0a4aa8570971ef29b952873e9e3d59e15 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:49 +0200
Subject: gnu: r-bionet: Update to 1.56.0.

* gnu/packages/bioconductor.scm (r-bionet): Update to 1.56.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3e80b2ab8b..9bf94f9ff4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15704,14 +15704,14 @@ (define-public r-bionero
 (define-public r-bionet
   (package
     (name "r-bionet")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNet" version))
        (sha256
         (base32
-         "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg"))))
+         "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
     (properties `((upstream-name . "BioNet")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From dba6a33e3d57128442f1c5bf63e1c57f7391a013 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:49 +0200
Subject: gnu: r-bionetstat: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-bionetstat): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9bf94f9ff4..7818d39295 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15733,14 +15733,14 @@ (define-public r-bionet
 (define-public r-bionetstat
   (package
     (name "r-bionetstat")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioNetStat" version))
        (sha256
         (base32
-         "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8"))))
+         "0f387j35lj32ryiw48jz8gc08al2lmmv9zvbbgyjq9wmqlca3dfb"))))
     (properties `((upstream-name . "BioNetStat")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e8e3d333f0fd45904a692b8cde8364a8a88528c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:49 +0200
Subject: gnu: r-bioqc: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7818d39295..346c15acfa 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15775,14 +15775,14 @@ (define-public r-bionetstat
 (define-public r-bioqc
   (package
     (name "r-bioqc")
-    (version "1.22.0")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioQC" version))
        (sha256
         (base32
-         "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407"))))
+         "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
     (properties `((upstream-name . "BioQC")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4b3f9a16f2b7a3db728e11747366d1cb94039489 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:49 +0200
Subject: gnu: r-biotip: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-biotip): Update to 1.10.0.
[propagated-inputs]: Remove r-hmisc; add r-scran.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 346c15acfa..3a65c554a5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15801,23 +15801,23 @@ (define-public r-bioqc
 (define-public r-biotip
   (package
     (name "r-biotip")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BioTIP" version))
        (sha256
         (base32
-         "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys"))))
+         "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
     (properties `((upstream-name . "BioTIP")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-cluster
            r-genomicranges
-           r-hmisc
            r-igraph
            r-mass
            r-psych
+           r-scran
            r-stringr))
     (native-inputs
      (list r-knitr))
-- 
cgit v1.2.3


From 397bdc4329bbefc31b6b37216955bcae7d987577 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:50 +0200
Subject: gnu: r-biotmle: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.20.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3a65c554a5..509e3305ab 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15831,14 +15831,14 @@ (define-public r-biotip
 (define-public r-biotmle
   (package
     (name "r-biotmle")
-    (version "1.18.0")
+    (version "1.20.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biotmle" version))
        (sha256
         (base32
-         "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g"))))
+         "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
     (properties `((upstream-name . "biotmle")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 4ab8327ba4ac42bbf39fffe6cddf9ae61e1d73be Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:50 +0200
Subject: gnu: r-bsseq: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 509e3305ab..a672997607 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15873,14 +15873,14 @@ (define-public r-biotmle
 (define-public r-bsseq
   (package
     (name "r-bsseq")
-    (version "1.30.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bsseq" version))
        (sha256
         (base32
-         "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d"))))
+         "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
     (properties `((upstream-name . "bsseq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From b1c215755a952bd058c97c885d159401887135da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:50 +0200
Subject: gnu: r-dmrseq: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a672997607..982902e210 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15919,14 +15919,14 @@ (define-public r-bsseq
 (define-public r-dmrseq
   (package
     (name "r-dmrseq")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "dmrseq" version))
        (sha256
         (base32
-         "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd"))))
+         "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
     (properties `((upstream-name . "dmrseq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 6f31f4618a20d5702c08324cd61fa2ef72ac366d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:50 +0200
Subject: gnu: r-omnipathr: Update to 3.4.0.

* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.4.0.
[propagated-inputs]: Add r-withr.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 982902e210..f651b33ebe 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15965,13 +15965,13 @@ (define-public r-dmrseq
 (define-public r-omnipathr
   (package
     (name "r-omnipathr")
-    (version "3.2.8")
+    (version "3.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "OmnipathR" version))
        (sha256
-        (base32 "0vr16ar3rbjsfw4qz2g86lbhvmqwgq0vcahc6vrc4d9rdjxwg6sb"))))
+        (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
     (properties `((upstream-name . "OmnipathR")))
     (build-system r-build-system)
     (arguments
@@ -16001,6 +16001,7 @@ (define-public r-omnipathr
            r-tibble
            r-tidyr
            r-tidyselect
+           r-withr
            r-xml2
            r-yaml))
     (native-inputs (list r-knitr))
-- 
cgit v1.2.3


From a4f03b0a55f2fcdddc45802948c2c3358894e466 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:50 +0200
Subject: gnu: r-biscuiteer: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.10.0.
[propagated-inputs]: Add r-iranges.
---
 gnu/packages/bioconductor.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f651b33ebe..2d6de0e259 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16018,14 +16018,14 @@ (define-public r-omnipathr
 (define-public r-biscuiteer
   (package
     (name "r-biscuiteer")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biscuiteer" version))
        (sha256
         (base32
-         "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj"))))
+         "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
     (properties `((upstream-name . "biscuiteer")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16043,6 +16043,7 @@ (define-public r-biscuiteer
            r-hdf5array
            r-homo-sapiens
            r-impute
+           r-iranges
            r-matrix
            r-matrixstats
            r-mus-musculus
-- 
cgit v1.2.3


From 5ec7143f69b2d567683d6901754051f147fd495c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:50 +0200
Subject: gnu: r-tcgabiolinks: Update to 2.24.1.

* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.24.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2d6de0e259..c2c8b654da 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16070,13 +16070,13 @@ (define-public r-biscuiteer
 (define-public r-tcgabiolinks
   (package
     (name "r-tcgabiolinks")
-    (version "2.22.4")
+    (version "2.24.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TCGAbiolinks" version))
        (sha256
-        (base32 "071wz6dm6dypbfzvxd6j67l1iawlb6d5sfzq871zh06fzaxjm332"))))
+        (base32 "0kw4lrg8xm0ipj7f7h1rwfj7a8mknkril1pn05x08mx13f7p5p14"))))
     (properties `((upstream-name . "TCGAbiolinks")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e290d834d908c95b7cde9d5fffb10ad781cc8f50 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:51 +0200
Subject: gnu: r-tricycle: Update to 1.4.0.

* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.4.0.
[propagated-inputs]: Add r-ggnewscale.
---
 gnu/packages/bioconductor.scm | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c2c8b654da..6bdeaf0a67 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16125,27 +16125,29 @@ (define-public r-tcgabiolinks
 (define-public r-tricycle
   (package
     (name "r-tricycle")
-    (version "1.2.1")
+    (version "1.4.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "tricycle" version))
               (sha256
                (base32
-                "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r"))))
+                "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
     (properties `((upstream-name . "tricycle")))
     (build-system r-build-system)
-    (propagated-inputs (list r-annotationdbi
-                             r-circular
-                             r-dplyr
-                             r-genomicranges
-                             r-ggplot2
-                             r-iranges
-                             r-rcolorbrewer
-                             r-s4vectors
-                             r-scater
-                             r-scattermore
-                             r-singlecellexperiment
-                             r-summarizedexperiment))
+    (propagated-inputs
+     (list r-annotationdbi
+           r-circular
+           r-dplyr
+           r-genomicranges
+           r-ggnewscale
+           r-ggplot2
+           r-iranges
+           r-rcolorbrewer
+           r-s4vectors
+           r-scater
+           r-scattermore
+           r-singlecellexperiment
+           r-summarizedexperiment))
     (native-inputs (list r-knitr))
     (home-page "https://github.com/hansenlab/tricycle")
     (synopsis "Transferable representation and inference of cell cycle")
-- 
cgit v1.2.3


From e0be852a1ea00ec9b44e7df722021252fe5643d5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:51 +0200
Subject: gnu: r-tximeta: Update to 1.14.0.

* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.14.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6bdeaf0a67..7c27ace453 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16164,14 +16164,14 @@ (define-public r-tricycle
 (define-public r-tximeta
   (package
     (name "r-tximeta")
-    (version "1.12.4")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "tximeta" version))
        (sha256
         (base32
-         "1lm2r64d6sdfzvxcabgs0214cdc5dl9pfx562acjcxz5mb101g9g"))))
+         "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl"))))
     (properties `((upstream-name . "tximeta")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 319fa58dac2499525c1e340ee7bb3200f1c37239 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 12:46:51 +0200
Subject: gnu: r-phyloseq: Update to 1.40.0.

* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.40.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c27ace453..5d94d25d5d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16205,13 +16205,13 @@ (define-public r-tximeta
 (define-public r-phyloseq
   (package
     (name "r-phyloseq")
-    (version "1.38.0")
+    (version "1.40.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "phyloseq" version))
        (sha256
-        (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s"))))
+        (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
     (properties `((upstream-name . "phyloseq")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 549a9e6f6a86a72af4733ca22280c3b5a29acc0a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:20 +0200
Subject: gnu: r-leidenbase: Update to 0.1.9.

* gnu/packages/bioconductor.scm (r-leidenbase): Update to 0.1.9.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5d94d25d5d..e1cc32d8fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7652,11 +7652,11 @@ (define-public r-monocle
     (license license:artistic2.0)))
 
 (define-public r-leidenbase
-  (let ((commit "430f22af6982cc7d2e6e77f6b0df47bc970dcbce")
+  (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
         (revision "1"))
     (package
       (name "r-leidenbase")
-      (version (git-version "0.1.3" revision commit))
+      (version (git-version "0.1.9" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -7666,7 +7666,7 @@ (define-public r-leidenbase
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0ylqsmdpv4xq6f6ldxvwkhk33a9i1jcgk60zvksk3iplykfzd6c0"))))
+           "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
       (properties `((upstream-name . "leidenbase")))
       (build-system r-build-system)
       (inputs
-- 
cgit v1.2.3


From 3d93251ea58129c3dac450b3ace76a7e9549efc7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:54 +0200
Subject: gnu: r-bsgenome-hsapiens-ucsc-hg19: Update to 1.4.3.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): Update to 1.4.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e1cc32d8fd..02c8612b23 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -696,14 +696,14 @@ (define-public r-org-mm-eg-db
 (define-public r-bsgenome-hsapiens-ucsc-hg19
   (package
     (name "r-bsgenome-hsapiens-ucsc-hg19")
-    (version "1.4.0")
+    (version "1.4.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
                                      version 'annotation))
               (sha256
                (base32
-                "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
+                "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 8ee1246a38649d0a57b8f36161a4744f8efe16f6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:54 +0200
Subject: gnu: r-bsgenome-hsapiens-ucsc-hg38: Update to 1.4.4.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38): Update to 1.4.4.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 02c8612b23..0211ccdc41 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -720,14 +720,13 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19
 (define-public r-bsgenome-hsapiens-ucsc-hg38
   (package
     (name "r-bsgenome-hsapiens-ucsc-hg38")
-    (version "1.4.1")
+    (version "1.4.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
                                      version 'annotation))
               (sha256
-               (base32
-                "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
+               (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 5efae7b049ed2747061058c1aaf50a1aeef24cca Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:55 +0200
Subject: gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Update to 3.15.0.

* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene): Update to 3.15.0.
[propagated-inputs]: Add r-annotationdbi.
---
 gnu/packages/bioconductor.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0211ccdc41..88b697d4ff 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -891,19 +891,18 @@ (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
   (package
     (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
-    (version "3.4.6")
+    (version "3.15.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
                                      version 'annotation))
               (sha256
-               (base32
-                "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
+               (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879"))))
     (properties
      `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-genomicfeatures))
+     (list r-annotationdbi r-genomicfeatures))
     (home-page
      "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
     (synopsis "Annotation package for human genome in TxDb format")
-- 
cgit v1.2.3


From 7feae8098c5effe4428840f594d3a149c06ee56a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:55 +0200
Subject: gnu: r-pfam-db: Update to 3.15.0.

* gnu/packages/bioconductor.scm (r-pfam-db): Update to 3.15.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 88b697d4ff..88a5742689 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1079,14 +1079,13 @@ (define-public r-hgu133plus2-db
 (define-public r-pfam-db
   (package
     (name "r-pfam-db")
-    (version "3.8.2")
+    (version "3.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "PFAM.db" version 'annotation))
        (sha256
-        (base32
-         "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
+        (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7"))))
     (properties `((upstream-name . "PFAM.db")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c89eb68ede7ea479e43374ce1b2ee0526333aa7c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:55 +0200
Subject: gnu: r-adductdata: Update to 1.12.0.

* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.12.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 88a5742689..9bc23d2f72 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1166,13 +1166,12 @@ (define-public r-abadata
 (define-public r-adductdata
   (package
     (name "r-adductdata")
-    (version "1.10.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "adductData" version 'experiment))
               (sha256
-               (base32
-                "0bp74p06gskwn2xl1srpnmsq27ajsrlynkzw6fcmvwwjcrzljmnj"))))
+               (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48"))))
     (properties `((upstream-name . "adductData")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationhub r-experimenthub))
-- 
cgit v1.2.3


From 9db43e49792329806ecbdcfa30f28c0931835157 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:55 +0200
Subject: gnu: r-aneufinderdata: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-aneufinderdata): Update to 1.24.0.
---
 gnu/packages/bioconductor.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9bc23d2f72..36cf206263 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1187,17 +1187,17 @@ (define-public r-adductdata
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")
-   (version "1.18.0")
+   (version "1.24.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "AneuFinderData" version 'experiment))
             (sha256
-             (base32
-              "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks"))))
+             (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7"))))
    (build-system r-build-system)
    (home-page "https://bioconductor.org/packages/AneuFinderData/")
    (synopsis "Data package for @code{AneuFinder}")
-   (description "This package contains data used by @code{AneuFinder}.")
+   (description "This package contains whole-genome single cell sequencing data for
+demonstration purposes in the @code{AneuFinder} package.")
    (license license:artistic2.0)))
 
 (define-public r-arrmdata
-- 
cgit v1.2.3


From ccb66a16a06fdfc764560665858e62caf41e552b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:55 +0200
Subject: gnu: r-arrmdata: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-arrmdata): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 36cf206263..6eae1e1686 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1203,13 +1203,12 @@ (define-public r-aneufinderdata
 (define-public r-arrmdata
   (package
     (name "r-arrmdata")
-    (version "1.18.0")
+    (version "1.32.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "ARRmData" version 'experiment))
               (sha256
-               (base32
-                "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
+               (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p"))))
     (properties
      `((upstream-name . "ARRmData")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3ce819d5635aff3540f55dd0bcc13e034a72c67d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:55 +0200
Subject: gnu: r-biscuiteerdata: Update to 1.10.0.

* gnu/packages/bioconductor.scm (r-biscuiteerdata): Update to 1.10.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6eae1e1686..401461bfac 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1222,14 +1222,13 @@ (define-public r-arrmdata
 (define-public r-biscuiteerdata
   (package
     (name "r-biscuiteerdata")
-    (version "1.6.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biscuiteerData" version 'experiment))
        (sha256
-        (base32
-         "1d7zibjf0qccmdnzdxh7wy1h943yhnbf8zdix72486pvhzm124zj"))))
+        (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
     (properties
      `((upstream-name . "biscuiteerData")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 1413f9f214cb8ac8e23db87d3be642da79385a55 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-celldex: Update to 1.6.0.

* gnu/packages/bioconductor.scm (r-celldex): Update to 1.6.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 401461bfac..a57cf52957 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1245,13 +1245,13 @@ (define-public r-biscuiteerdata
 (define-public r-celldex
   (package
     (name "r-celldex")
-    (version "1.4.0")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "celldex" version 'experiment))
        (sha256
-        (base32 "04w60fx3s3wlirmr65nsz6d7ig48j9fzimdr8kbdqv1g80ivdcq1"))))
+        (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
     (properties `((upstream-name . "celldex")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e437cf10a45e69b332234c13335db5dc7a4a07ff Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-chromstardata: Update to 1.22.0.

* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.22.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a57cf52957..3dd66890d7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1274,14 +1274,13 @@ (define-public r-celldex
 (define-public r-chromstardata
   (package
     (name "r-chromstardata")
-    (version "1.16.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "chromstaRData" version 'experiment))
        (sha256
-        (base32
-         "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
+        (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
     (properties `((upstream-name . "chromstaRData")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/chromstaRData/")
-- 
cgit v1.2.3


From 7a58c9af46041ee069d8143549431bcde08bc2f8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-copyhelper: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-copyhelper): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3dd66890d7..651bdec63d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1293,14 +1293,13 @@ (define-public r-chromstardata
 (define-public r-copyhelper
   (package
     (name "r-copyhelper")
-    (version "1.6.0")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
        (sha256
-        (base32
-         "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+        (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
     (properties `((upstream-name . "CopyhelpeR")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/CopyhelpeR/")
-- 
cgit v1.2.3


From d24b0702b60e7052eabcd2f94b6682ad29b24c1d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-genelendatabase: Update to 1.32.0.

* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.32.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 651bdec63d..48dd1b6231 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1316,14 +1316,13 @@ (define-public r-copyhelper
 (define-public r-genelendatabase
   (package
     (name "r-genelendatabase")
-    (version "1.18.0")
+    (version "1.32.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
        (sha256
-        (base32
-         "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
+        (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
     (properties
      `((upstream-name . "geneLenDataBase")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 4f2ac5f19f23be9b5a3bbf762111b0d4cf2f6d9d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-genomationdata: Update to 1.28.0.

* gnu/packages/bioconductor.scm (r-genomationdata): Update to 1.28.0.
---
 gnu/packages/bioconductor.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 48dd1b6231..d17389e2ef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1338,13 +1338,13 @@ (define-public r-genelendatabase
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "genomationData" version 'experiment))
-              (sha256
-               (base32
-                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "genomationData" version 'experiment))
+       (sha256
+        (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
     (properties
      `((upstream-name . "genomationData")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 3ff4e48e85be24316756515ad4f4680079e14266 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-pasilla: Update to 1.24.0.

* gnu/packages/bioconductor.scm (r-pasilla): Update to 1.24.0.
[propagated-inputs]: Remove r-biocstyle, r-knitr, and r-rmarkdown.
[native-inputs]: Add r-knitr.
---
 gnu/packages/bioconductor.scm | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d17389e2ef..8329c4feb9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1364,16 +1364,16 @@ (define-public r-genomationdata
 (define-public r-pasilla
   (package
     (name "r-pasilla")
-    (version "1.14.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "pasilla" version 'experiment))
-              (sha256
-               (base32
-                "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "pasilla" version 'experiment))
+       (sha256
+        (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
     (build-system r-build-system)
-    (propagated-inputs
-     (list r-biocstyle r-dexseq r-knitr r-rmarkdown))
+    (propagated-inputs (list r-dexseq))
+    (native-inputs (list r-knitr))
     (home-page "https://www.bioconductor.org/packages/pasilla/")
     (synopsis "Data package with per-exon and per-gene read counts")
     (description "This package provides per-exon and per-gene read counts
-- 
cgit v1.2.3


From 15e10974ef22940242623377e46fb3e56b56ae6e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-hsmmsinglecell: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-hsmmsinglecell): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8329c4feb9..f31879bbb6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1385,13 +1385,13 @@ (define-public r-pasilla
 (define-public r-hsmmsinglecell
   (package
     (name "r-hsmmsinglecell")
-    (version "1.2.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
-              (sha256
-               (base32
-                "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
+    (version "1.16.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
+       (sha256
+        (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
     (properties
      `((upstream-name . "HSMMSingleCell")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From e06ee7a745ed82d349e111a103abacb957324042 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:56 +0200
Subject: gnu: r-all: Update to 1.38.0.

* gnu/packages/bioconductor.scm (r-all): Update to 1.38.0.
---
 gnu/packages/bioconductor.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f31879bbb6..a60e621ac4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1414,13 +1414,13 @@ (define-public r-hsmmsinglecell
 (define-public r-all
   (package
     (name "r-all")
-    (version "1.26.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "ALL" version 'experiment))
-              (sha256
-               (base32
-                "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ALL" version 'experiment))
+       (sha256
+        (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
     (properties `((upstream-name . "ALL")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From c56b553e97777dccc2619b5c75525d745b2641e7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:57 +0200
Subject: gnu: r-affydata: Update to 1.44.0.

* gnu/packages/bioconductor.scm (r-affydata): Update to 1.44.0.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a60e621ac4..e643513b89 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1438,14 +1438,13 @@ (define-public r-all
 (define-public r-affydata
   (package
     (name "r-affydata")
-    (version "1.32.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affydata" version 'experiment))
        (sha256
-        (base32
-         "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
+        (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
     (properties `((upstream-name . "affydata")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 1c4d0fc9a9d3c324f930b04d6c230154db6da641 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:57 +0200
Subject: gnu: r-gagedata: Update to 2.34.0.

* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.34.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e643513b89..b4ce9d6f9e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1460,13 +1460,13 @@ (define-public r-affydata
 (define-public r-gagedata
   (package
     (name "r-gagedata")
-    (version "2.28.0")
+    (version "2.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gageData" version 'experiment))
        (sha256
-        (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
+        (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
     (properties `((upstream-name . "gageData")))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/gageData")
-- 
cgit v1.2.3


From 9d538de266257307c0072253c001bb1302372596 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:57 +0200
Subject: gnu: r-curatedtcgadata: Update to 1.18.0.

* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.18.0.
[native-inputs]: Add r-knitr.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b4ce9d6f9e..aa980ed9b4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1486,14 +1486,13 @@ (define-public r-gagedata
 (define-public r-curatedtcgadata
   (package
     (name "r-curatedtcgadata")
-    (version "1.8.0")
+    (version "1.18.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
        (sha256
-        (base32
-         "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
+        (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
     (properties
      `((upstream-name . "curatedTCGAData")))
     (build-system r-build-system)
@@ -1504,6 +1503,7 @@ (define-public r-curatedtcgadata
            r-multiassayexperiment
            r-s4vectors
            r-summarizedexperiment))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/curatedTCGAData/")
     (synopsis "Curated data from The Cancer Genome Atlas")
     (description
-- 
cgit v1.2.3


From 79158a5624a587395e36125ad5d0cc369c841af4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 15:16:57 +0200
Subject: gnu: r-tcgabiolinksgui-data: Update to 1.16.0.

* gnu/packages/bioconductor.scm (r-tcgabiolinksgui-data): Update to 1.16.0.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aa980ed9b4..be946ae667 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1519,13 +1519,13 @@ (define-public r-curatedtcgadata
 (define-public r-tcgabiolinksgui-data
   (package
     (name "r-tcgabiolinksgui-data")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
        (sha256
-        (base32 "08zmlvycq3jz1zy0715x9f21nf3465c51k7w2jq12sfbap36pmjm"))))
+        (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
     (properties `((upstream-name . "TCGAbiolinksGUI.data")))
     (build-system r-build-system)
     (native-inputs (list r-knitr))
-- 
cgit v1.2.3


From 66bfe558481a2431810d7a2d2436d06d6f8daab7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 28 May 2022 17:03:02 +0200
Subject: gnu: Add r-msdata.

* gnu/packages/bioconductor.scm (r-msdata): New variable.
---
 gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index be946ae667..518224306f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1361,6 +1361,29 @@ (define-public r-genomationdata
 downloaded from Encode.")
     (license license:gpl3+)))
 
+(define-public r-msdata
+  (package
+    (name "r-msdata")
+    (version "0.36.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "msdata" version 'experiment))
+       (sha256
+        (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
+    (properties `((upstream-name . "msdata")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/msdata")
+    (synopsis "Various Mass Spectrometry raw data example files")
+    (description
+     "This package provides Ion Trap positive ionization mode data in mzML file
+format.  It includes a subset from 500-850 m/z and 1190-1310 seconds,
+including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
+III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
+LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
+files for various search engines.")
+    (license license:gpl2+)))
+
 (define-public r-pasilla
   (package
     (name "r-pasilla")
-- 
cgit v1.2.3


From a5f4c03df18f8f76d570b996399a4adf0fc297c6 Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Fri, 27 May 2022 18:40:13 +0200
Subject: gnu: Add r-scmap.

* gnu/packages/bioconductor.scm (r-scmap): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4baa80dcb1..1962117132 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5049,6 +5049,48 @@ (define-public r-scdblfinder
 comprehensive scDblFinder method.")
     (license license:gpl3)))
 
+(define-public r-scmap
+  (package
+    (name "r-scmap")
+    (version "1.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scmap" version))
+       (sha256
+        (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
+    (properties `((upstream-name . "scmap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-dplyr
+           r-e1071
+           r-ggplot2
+           r-googlevis
+           r-matrixstats
+           r-proxy
+           r-randomforest
+           r-rcpp
+           r-rcpparmadillo
+           r-reshape2
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hemberg-lab/scmap")
+    (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
+    (description
+     "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
+composition of complex tissues since the technology allows researchers to
+define cell-types using unsupervised clustering of the transcriptome.
+However, due to differences in experimental methods and computational
+analyses, it is often challenging to directly compare the cells identified in
+two different experiments.  @code{scmap} is a method for projecting cells from
+a scRNA-seq experiment onto the cell-types or individual cells identified in a
+different experiment.")
+    (license license:gpl3)))
+
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-- 
cgit v1.2.3


From 89e926201234a4fe5474dc97504474323dd03f0a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 29 May 2022 11:44:09 +0200
Subject: gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Update to 1.3.993.

* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): Update to 1.3.993.
---
 gnu/packages/bioconductor.scm | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 518224306f..59b921af82 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -358,14 +358,14 @@ (define-public r-bsgenome-hsapiens-ncbi-grch38
 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
   (package
     (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
-    (version "1.3.99")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
-                                     version 'annotation))
-              (sha256
-               (base32
-                "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
+    (version "1.3.993")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
+                              version 'annotation))
+       (sha256
+        (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From bfcae1efbb524e8d4ea404ba5985d5219ac63612 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 30 May 2022 15:16:35 +0200
Subject: gnu: r-batchelor: Update to 1.12.1.

* gnu/packages/bioconductor.scm (r-batchelor): Update to 1.12.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4d3f86bfd3..176f7ecc6d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7574,14 +7574,14 @@ (define-public r-residualmatrix
 (define-public r-batchelor
   (package
     (name "r-batchelor")
-    (version "1.10.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "batchelor" version))
        (sha256
         (base32
-         "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr"))))
+         "1zyvjr9nwfh0cdqk4kwmr30yhh05picyab1hpnpn737xvn525jfi"))))
     (properties `((upstream-name . "batchelor")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3