From bb15b581f74dbf4f06425e3ef0aae1863adca377 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:24:23 +0200 Subject: gnu: Add r-bayseq. * gnu/packages/bioconductor.scm (r-bayseq): New variable. --- 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 ed35b4c61a..3dba9cbab4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -371,3 +371,29 @@ (define-public r-qdnaseq segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.") (license license:gpl2+))) + +(define-public r-bayseq + (package + (name "r-bayseq") + (version "2.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "baySeq" version)) + (sha256 + (base32 + "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg")))) + (properties `((upstream-name . "baySeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-edger" ,r-edger) + ("r-genomicranges" ,r-genomicranges))) + (home-page "https://bioconductor.org/packages/baySeq/") + (synopsis "Bayesian analysis of differential expression patterns in count data") + (description + "This package identifies differential expression in high-throughput count +data, such as that derived from next-generation sequencing machines, +calculating estimated posterior likelihoods of differential expression (or +more complex hypotheses) via empirical Bayesian methods.") + (license license:gpl3))) -- cgit v1.2.3 From dfac7eb9170ae3b93ca2c179c13b33bc1ae7023d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:26:48 +0200 Subject: gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked. * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked): 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 3dba9cbab4..7685cee9e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -61,6 +61,41 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm6 objects.") (license license:artistic2.0))) +(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked + (package + (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") + (version "1.3.99") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Dmelanogaster.UCSC.dm3.masked_" + version ".tar.gz")) + (sha256 + (base32 + "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) + (properties + `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-dmelanogaster-ucsc-dm3" + ,r-bsgenome-dmelanogaster-ucsc-dm3))) + (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") + (synopsis "Full masked genome sequences for Fly") + (description + "This package provides full masked genome sequences for Drosophila +melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in +Biostrings objects. The sequences are the same as in +BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following +masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of +intra-contig ambiguities (AMB mask), (3) the mask of repeats from +RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats +Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") -- cgit v1.2.3 From 6fbd759b132d65825bfeb47ac66a957bde38c770 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:27:10 +0200 Subject: gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked. * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): 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 7685cee9e5..e1a1ba1963 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -96,6 +96,41 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) +(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) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Hsapiens.UCSC.hg19.masked_" + version ".tar.gz")) + (sha256 + (base32 + "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) + (properties + `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" + ,r-bsgenome-hsapiens-ucsc-hg19))) + (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") + (synopsis "Full masked genome sequences for Homo sapiens") + (description + "This package provides full genome sequences for Homo sapiens (Human) as +provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The +sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of +them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS +mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of +repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem +Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by +default.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") -- cgit v1.2.3 From 2bece692a685d4a4e823cf908898a2aceaadc6c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:27:29 +0200 Subject: gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked. * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): 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 e1a1ba1963..e962ad523e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -131,6 +131,41 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19-masked default.") (license license:artistic2.0))) +(define-public r-bsgenome-mmusculus-ucsc-mm9-masked + (package + (name "r-bsgenome-mmusculus-ucsc-mm9-masked") + (version "1.3.99") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Mmusculus.UCSC.mm9.masked_" + version ".tar.gz")) + (sha256 + (base32 + "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) + (properties + `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-mmusculus-ucsc-mm9" + ,r-bsgenome-mmusculus-ucsc-mm9))) + (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") + (synopsis "Full masked genome sequences for Mouse") + (description + "This package provides full genome sequences for Mus musculus (Mouse) as +provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The +sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of +them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS +mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of +repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem +Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by +default." ) + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") -- cgit v1.2.3 From 609f4ad12fb37e256d6bb2b89cb2c1a8b30bd28c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:36:15 +0200 Subject: gnu: Add r-chipcomp. * gnu/packages/bioconductor.scm (r-chipcomp): New variable. --- 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 e962ad523e..93d68c2a5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -502,3 +502,37 @@ (define-public r-bayseq calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.") (license license:gpl3))) + +(define-public r-chipcomp + (package + (name "r-chipcomp") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPComp" version)) + (sha256 + (base32 + "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs")))) + (properties `((upstream-name . "ChIPComp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/ChIPComp") + (synopsis "Quantitative comparison of multiple ChIP-seq datasets") + (description + "ChIPComp implements a statistical method for quantitative comparison of +multiple ChIP-seq datasets. It detects differentially bound sharp binding +sites across multiple conditions considering matching control in ChIP-seq +datasets.") + ;; Any version of the GPL. + (license license:gpl3+))) -- cgit v1.2.3 From 0490f9de88edef1947c6e047701a86bf1b37a506 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:38:17 +0200 Subject: gnu: Add r-riboprofiling. * gnu/packages/bioconductor.scm (r-riboprofiling): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 93d68c2a5f..8dbbb74b3f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -536,3 +536,42 @@ (define-public r-chipcomp datasets.") ;; Any version of the GPL. (license license:gpl3+))) + +(define-public r-riboprofiling + (package + (name "r-riboprofiling") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RiboProfiling" version)) + (sha256 + (base32 + "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0")))) + (properties `((upstream-name . "RiboProfiling"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-sqldf" ,r-sqldf))) + (home-page "https://bioconductor.org/packages/RiboProfiling/") + (synopsis "Ribosome profiling data analysis") + (description "Starting with a BAM file, this package provides the +necessary functions for quality assessment, read start position recalibration, +the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting +of count data: pairs, log fold-change, codon frequency and coverage +assessment, principal component analysis on codon coverage.") + (license license:gpl3))) -- cgit v1.2.3 From 6ffdfe6a0121f6e9e6029ef16d1653afc49628d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:38:27 +0200 Subject: gnu: Add r-riboseqr. * gnu/packages/bioconductor.scm (r-riboseqr): 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 8dbbb74b3f..634493d136 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -575,3 +575,31 @@ (define-public r-riboprofiling of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.") (license license:gpl3))) + +(define-public r-riboseqr + (package + (name "r-riboseqr") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "riboSeqR" version)) + (sha256 + (base32 + "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn")))) + (properties `((upstream-name . "riboSeqR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-bayseq" ,r-bayseq) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-seqlogo" ,r-seqlogo))) + (home-page "https://bioconductor.org/packages/riboSeqR/") + (synopsis "Analysis of sequencing data from ribosome profiling experiments") + (description + "This package provides plotting functions, frameshift detection and +parsing of genetic sequencing data from ribosome profiling experiments.") + (license license:gpl3))) -- cgit v1.2.3 From a32279ffb68a23458177bf6a9b9cae5abea59e2e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 08:21:01 +0200 Subject: gnu: Add r-interactionset. * gnu/packages/bioconductor.scm (r-interactionset): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 634493d136..771f6a46d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -603,3 +603,35 @@ (define-public r-riboseqr "This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments.") (license license:gpl3))) + +(define-public r-interactionset + (package + (name "r-interactionset") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "InteractionSet" version)) + (sha256 + (base32 + "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n")))) + (properties + `((upstream-name . "InteractionSet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/InteractionSet") + (synopsis "Base classes for storing genomic interaction data") + (description + "This packages provides the @code{GInteractions}, +@code{InteractionSet} and @code{ContactMatrix} objects and associated methods +for storing and manipulating genomic interaction data from Hi-C and ChIA-PET +experiments.") + (license license:gpl3))) -- cgit v1.2.3 From cf9a29b24c990aeadb673d233b3ca686249b2b10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 08:21:17 +0200 Subject: gnu: Add r-genomicinteractions. * gnu/packages/bioconductor.scm (r-genomicinteractions): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 42 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 771f6a46d1..a6a8216ccb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -24,10 +24,11 @@ (define-module (gnu packages bioconductor) #:use-module (guix download) #:use-module (guix build-system r) #:use-module (gnu packages) + #:use-module (gnu packages bioinformatics) #:use-module (gnu packages cran) #:use-module (gnu packages compression) - #:use-module (gnu packages statistics) - #:use-module (gnu packages bioinformatics)) + #:use-module (gnu packages graph) + #:use-module (gnu packages statistics)) (define-public r-bsgenome-dmelanogaster-ucsc-dm6 (package @@ -635,3 +636,42 @@ (define-public r-interactionset for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.") (license license:gpl3))) + +(define-public r-genomicinteractions + (package + (name "r-genomicinteractions") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicInteractions" version)) + (sha256 + (base32 + "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q")))) + (properties + `((upstream-name . "GenomicInteractions"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gviz" ,r-gviz) + ("r-igraph" ,r-igraph) + ("r-interactionset" ,r-interactionset) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") + (synopsis "R package for handling genomic interaction data") + (description + "This R package provides tools for handling genomic interaction data, +such as ChIA-PET/Hi-C, annotating genomic features with interaction +information and producing various plots and statistics.") + (license license:gpl3))) -- cgit v1.2.3