diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 604 |
1 files changed, 545 insertions, 59 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 711b988e7f..2bfca85bbc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -33,6 +33,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) @@ -115,6 +116,33 @@ analysis.") based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) +(define-public r-pd-mapping50k-xba240 + (package + (name "r-pd-mapping50k-xba240") + (version "3.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pd.mapping50k.xba240" version + 'annotation)) + (sha256 + (base32 "1a1f3lh5ywhyjawdbj2fzban85c8jz70lfcv3pagd5piincjwxq8")))) + (properties `((upstream-name . "pd.mapping50k.xba240"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-dbi + r-iranges + r-oligo + r-oligoclasses + r-rsqlite + r-s4vectors)) + (home-page "https://bioconductor.org/packages/pd.mapping50k.xba240") + (synopsis "Platform design info for Affymetrix Mapping50K_Xba240") + (description "This package provides platform design info for Affymetrix +Mapping50K_Xba240 (pd.mapping50k.xba240).") + (license license:artistic2.0))) + (define-public r-reactome-db (package (name "r-reactome-db") @@ -1248,6 +1276,29 @@ demonstration purposes in the @code{AneuFinder} package.") from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-bcellviper + (package + (name "r-bcellviper") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bcellViper" version + 'experiment)) + (sha256 + (base32 + "1fpgh70x2r68v0ximgcdphnyzq2hgiwbamyhbac3yka8flhrd1fm")))) + (properties `((upstream-name . "bcellViper"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/bcellViper") + (synopsis + "Transcriptional interactome and normal human B-cell expression data") + (description + "This is a tool for human B-cell context-specific transcriptional +regulatory network. In addition, this package provides a human normal B-cells +dataset for the examples in package viper.") + (license license:gpl2+))) + (define-public r-bladderbatch (package (name "r-bladderbatch") @@ -1431,6 +1482,25 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-italicsdata + (package + (name "r-italicsdata") + (version "2.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ITALICSData" version 'experiment)) + (sha256 + (base32 "09d2igic3b5p7wpq98hb2lffxm1nfq9mwmnqlbdn3jv49pgz3hmw")))) + (properties `((upstream-name . "ITALICSData"))) + (build-system r-build-system) + (home-page "http://bioinfo.curie.fr") + (synopsis "ITALICS data") + (description "This package provides data needed to use the ITALICS +package.") + ;; Expanded from GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-macrophage (package (name "r-macrophage") @@ -1757,6 +1827,48 @@ expression level and gene-specific dispersion, that might facilitate the gene ranking by fold-change and visualization.") (license license:gpl3+))) +(define-public r-adacgh2 + (package + (name "r-adacgh2") + (version "2.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ADaCGH2" version)) + (sha256 + (base32 "0g9x3lnr56035wq9ijdcri4sz5pwj8184yxm415gmsxrii9xvpfd")))) + (properties `((upstream-name . "ADaCGH2"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'python3-compatibility + (lambda _ + (substitute* "inst/imagemap-example/toMap.py" + (("print nameMap") "print(nameMap)"))))))) + (inputs (list python-wrapper)) + (propagated-inputs + (list r-acgh + r-bit + r-cluster + r-dnacopy + r-ff + r-glad + r-snapcgh + r-tilingarray + r-waveslim)) + (home-page "https://github.com/rdiaz02/adacgh2") + (synopsis "Big data analysis from aCGH experiments") + (description + "This package analyzes and creates plots of array @acronym{CGH, +comparative genomic hybridization} data. Also, it allows usage of +@acronym{CBS, Circular Binary Segementation}, wavelet-based smoothing, HMM, +BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking +or with clusters, including MPI and sockets clusters) and use @code{ff} for +storing data.") + (license license:gpl3+))) + (define-public r-adam (package (name "r-adam") @@ -4467,6 +4579,37 @@ domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") (license license:gpl2+))) +(define-public r-italics + (package + (name "r-italics") + (version "2.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ITALICS" version)) + (sha256 + (base32 "0g937h9zxkxnm424wh58b46mfasdd7pqy5c04r0a46mx9lxibgbs")))) + (properties `((upstream-name . "ITALICS"))) + (build-system r-build-system) + (propagated-inputs + (list r-affxparser + r-dbi + r-glad + r-italicsdata + r-oligo + r-oligoclasses + r-pd-mapping50k-xba240)) + (home-page "http://bioinfo.curie.fr") + (synopsis "Normalizing of the Affymetrix GeneChip human mapping") + (description + "This package provides tools for normalizing and analyzing of GeneChip +Mapping 100K and 500K Set. Affymetrix GeneChip Human Mapping 100K and 500K +Set allows the DNA copy number mea- surement of respectively 2× 50K and 2× +250K SNPs along the genome. Their high density allows a precise localization +of genomic alterations and makes them a powerful tool for cancer and copy +number polymorphism study.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. (define-public r-absfiltergsea (package @@ -4605,7 +4748,7 @@ mapping.") r-stringr)) (native-inputs (list r-knitr)) - (home-page "http://renozao.github.io/NMF") + (home-page "https://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description "This package provides a framework to perform Non-negative Matrix @@ -4912,14 +5055,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.40.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x")))) + "16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5267,13 +5410,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.66.2") + (version "1.66.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0p75c52sw464bdqz7dyda9h8k2wsxdpdxxhya5awh977xaly90pf")))) + "1ps7s6i9mv8ys8k2xw8fdkh2rl2n3kcf2q4zsz6kcz5qpav95ys6")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -5439,6 +5582,57 @@ provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on r-complexheatmap from +;; Bioconductor. +(define-public r-conos + (package + (name "r-conos") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "conos" version)) + (sha256 + (base32 "1wdhb3jxh4id6xaghawzip8s264g9jxp4i5xy7jfhi67yfxszx6w")))) + (properties `((upstream-name . "conos"))) + (build-system r-build-system) + (propagated-inputs + (list r-abind + r-complexheatmap + r-cowplot + r-dendextend + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-igraph + r-irlba + r-leidenalg + r-magrittr + r-matrix + r-n2r + r-r6 + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress + r-reshape2 + r-rlang + r-rtsne + r-sccore)) + (home-page "https://github.com/kharchenkolab/conos") + (synopsis "Clustering on network of samples") + (description + "This package wires together large collections of single-cell RNA-seq +datasets, which allows for both the identification of recurrent cell clusters +and the propagation of information between datasets in multi-sample or +atlas-scale collections. Conos focuses on the uniform mapping of homologous +cell types across heterogeneous sample collections. For instance, users could +investigate a collection of dozens of peripheral blood samples from cancer +patients combined with dozens of controls, which perhaps includes samples of a +related tissue such as lymph nodes.") + (license license:gpl3))) + (define-public r-copywriter (package (name "r-copywriter") @@ -5513,14 +5707,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.38.2") + (version "1.38.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4")))) + "0kryg9jb6zl4zj1wx09rmljqlhr5vdbcmdnri4q91jpggsaj9nxm")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -5745,18 +5939,18 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.40.1") + (version "3.40.2") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg")))) + "0ds34b135qd63dh3cxkp8b28270m50bn1njwr49b8svgcgzz9x09")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit r-rcpp)) - (home-page "http://bioinf.wehi.edu.au/edgeR") + (home-page "https://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range @@ -5870,14 +6064,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.80.2") + (version "1.80.3") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq")))) + "047p84qxfqqm0d0ik7fxcs37fmg0yazsn9rz7h4g24cksb45p689")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5960,13 +6154,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.6") + (version "1.34.9") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "123kp69fmy5pbqh0j6qxdkvkm4g9pdwzms01i8qnix3m1b9j597w")))) + "0mn9ddm2xwc2b7zg0n9a056jcr61jv6v8jacxm3q8qmz6r30kfrb")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -6020,13 +6214,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.50.3") + (version "1.50.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz")))) + "1qsr433nh225pk5ngsrjrf2rfv7ynq4c8qsjfjr7khy2z9czlg6n")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -6122,6 +6316,30 @@ GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome.") (license license:artistic2.0))) +(define-public r-glad + (package + (name "r-glad") + (version "2.62.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GLAD" version)) + (sha256 + (base32 + "0gb52ic5r6nkgm2ynm174vcvbmkbhhjgv71lsmxpxzcsb6rr7qj6")))) + (properties `((upstream-name . "GLAD"))) + (build-system r-build-system) + (inputs (list gsl)) + (propagated-inputs (list r-aws)) + (native-inputs (list pkg-config)) + (home-page "http://bioinfo.curie.fr") + (synopsis "Gain and loss analysis of DNA") + (description + "This package helps with the analysis of array @acronym{CGH, comparative +genomic hybridization} data by detecting of the breakpoints in the genomic +profiles and assignment of a status (gain, normal or loss) to each chromosomal +regions identified.") + (license license:gpl2))) + (define-public r-gostats (package (name "r-gostats") @@ -6261,13 +6479,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.72.2") + (version "1.72.3") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv")))) + "1qq80za9bkg0wqnlckvahnjz08xacwvpnflwnrmwr2xg0ifkis38")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -6351,15 +6569,15 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.54.0") + (version "3.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma")))) + "0x6wkbw8v0hq9dfr433165jmii05rswjsm97dpxvyvxvya3sxqa1")))) (build-system r-build-system) - (home-page "http://bioinf.wehi.edu.au/limma") + (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") (description "This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments @@ -6367,6 +6585,73 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-maaslin2 + (package + (name "r-maaslin2") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Maaslin2" version)) + (sha256 + (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89")))) + (properties `((upstream-name . "Maaslin2"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'check 'remove-timestamps + (lambda _ + (with-directory-excursion + (string-append #$output "/site-library/Maaslin2/doc/demo_output/") + ;; Delete this log file with timestamps. + (delete-file "maaslin2.log") + ;; Replace PDF timestamps with an arbitrary fixed timestamp. + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* (find-files "." "\\.pdf$") + (("/CreationDate \\(D:.*\\)") + "/CreationDate (D:20230301143558)") + (("/ModDate \\(D:.*\\)") + "/ModDate (D:20230301143558)"))))))))) + (propagated-inputs + (list r-biglm + r-car + r-chemometrics + r-cplm + r-data-table + r-dplyr + r-edger + r-ggplot2 + r-glmmtmb + r-hash + r-lme4 + r-lmertest + r-logging + r-lpsymphony + r-mass + r-mumin + r-metagenomeseq + r-optparse + r-pbapply + r-pcapp + r-pheatmap + r-pscl + r-rmarkdown + r-robustbase + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "http://huttenhower.sph.harvard.edu/maaslin2") + (synopsis + "Multivariable association discovery in population-scale meta-omics studies") + (description + "MaAsLin2 is comprehensive R package for efficiently determining multivariable +association between clinical metadata and microbial meta'omic features. This +package relies on general linear models to accommodate most modern epidemiological +study designs, including cross-sectional and longitudinal, and offers a variety +of data exploration, normalization, and transformation methods.") + (license license:expat))) + (define-public r-made4 (package (name "r-made4") @@ -6423,6 +6708,29 @@ containing the location/probe set membership mapping. The other one creates a package that automatically loads that environment.") (license license:gpl2+))) +(define-public r-manor + (package + (name "r-manor") + (version "1.70.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MANOR" version)) + (sha256 + (base32 "16b30bmyzml97cjdbh6h9ky5c4h5ws2a3g2xkxnd55sd3jg64jgx")))) + (properties `((upstream-name . "MANOR"))) + (build-system r-build-system) + (propagated-inputs (list r-glad)) + (native-inputs (list r-knitr)) + (home-page "http://bioinfo.curie.fr/projects/manor/index.html") + (synopsis "CGH micro-array normalization") + (description + "This package ofers functions for importation, normalization, +visualization, and quality control to correct identified sources of +variability in array of @acronym{CGH, comparative genomic hybridization} +experiments.") + (license license:gpl2))) + (define-public r-maser (package (name "r-maser") @@ -6455,6 +6763,40 @@ package that automatically loads that environment.") and visualizaton of alternative splicing events generated by rMATS.") (license license:expat))) +(define-public r-metagenomeseq + (package + (name "r-metagenomeseq") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "metagenomeSeq" version)) + (sha256 + (base32 "01wjw4kcm8ysa5sn3cqg4a9i5pyksnwmbdqp5fr6n2l9hllkc9jy")))) + (properties `((upstream-name . "metagenomeSeq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-foreach + r-glmnet + r-gplots + r-limma + r-matrix + r-matrixstats + r-rcolorbrewer + r-wrench)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/HCBravoLab/metagenomeSeq") + (synopsis "Statistical analysis for sparse high-throughput sequencing") + (description + "MetagenomeSeq is designed to determine features (be it @acronym{OTU, +Operational Taxanomic Unit}, species, etc.) that are differentially abundant +between two or more groups of multiple samples. This package is designed to +address the effects of both normalization and under-sampling of microbial +communities on disease association detection and the testing of feature +correlations.") + (license license:artistic2.0))) + (define-public r-metaneighbor (package (name "r-metaneighbor") @@ -6661,6 +7003,37 @@ characterization and visualization of a wide range of mutational patterns in SNV base substitution data.") (license license:expat))) +(define-public r-msa + (package + (name "r-msa") + (version "1.30.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "msa" version)) + (sha256 + (base32 + "064hmry0zhmpchxgjsw0krsybr9v9gbsz26zmj2a39pg1nggwbq4")))) + (properties `((upstream-name . "msa"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-iranges + r-rcpp + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "http://www.bioinf.jku.at/software/msa/") + (synopsis "Multiple sequence alignment") + (description + "The msa package provides a unified R/Bioconductor interface to the +multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. +All three algorithms are integrated in the package, therefore, they do not +depend on any external software tools and are available for all major +platforms. The multiple sequence alignment algorithms are complemented by a +function for pretty-printing multiple sequence alignments using the LaTeX +package TeXshade.") + (license license:gpl2+))) + (define-public r-msnbase (package (name "r-msnbase") @@ -8003,13 +8376,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp")))) + (base32 "0qpss8fcf8ll47jv45ypsqd9jf7ajdiya7w4mw1wysk76spcwllm")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -8272,13 +8645,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.44.0") + (version "1.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8")))) + "13zim7dglsd5w39v22d2qa3d1h5dx33c1r4fz3vzri64kac0lhzx")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -8587,14 +8960,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.62.1") + (version "1.62.2") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz")))) + "19n0nvgyv2hzzcla93w2bzxvfdqg6walh0s1yykwl5b7ni4cazg9")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -8620,6 +8993,33 @@ arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (license license:lgpl2.0+))) +(define-public r-quantsmooth + (package + (name "r-quantsmooth") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "quantsmooth" version)) + (sha256 + (base32 "1adwws3brb01d4g6yidipnd8akkiyc3gpdr876hy57qnmcq8xipp")))) + (properties `((upstream-name . "quantsmooth"))) + (build-system r-build-system) + (propagated-inputs (list r-quantreg)) + (home-page "https://bioconductor.org/packages/quantsmooth") + (synopsis "Quantile smoothing and genomic visualization of array data") + (description + "This package implements quantile smoothing. It contains a dataset used +to produce human chromosomal ideograms for plotting purposes and a collection +of arrays that contains data of chromosome 14 of 3 colorectal tumors. The +package provides functions for painting chromosomal icons, chromosome or +chromosomal idiogram and other types of plots. Quantsmooth offers options +like converting chromosomal ids to their numeric form, retrieving the human +chromosomal length from NCBI data, retrieving regions of interest in a vector +of intensities using quantile smoothing, determining cytoband position based +on the location of the probe, and other useful tools.") + (license license:gpl2))) + (define-public r-qvalue (package (name "r-qvalue") @@ -9296,14 +9696,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w")))) + "1nk8jhabbrirpyjd1wdy2fjk8y2qi1bsjmgqzh0qi1c83n0ccz5d")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -9519,7 +9919,7 @@ in omics data.") (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) - (home-page "http://www.genopolis.it") + (home-page "https://www.genopolis.it") (synopsis "Detect differential expression in microarray and proteomics datasets") (description "The Power Law Global Error Model (PLGEM) has been shown to faithfully @@ -9977,14 +10377,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.72.2") + (version "1.72.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr")))) + "1kxzrny19dqd9pqj27vzr15i071sl8ivznpfd6zlqhcymlcsq7nw")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -10135,14 +10535,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.26.2") + (version "1.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3")))) + "0iqc6km4pw50li2q35km8jpa0p3i6a6way910wcz56yd2jjbjyz5")))) (build-system r-build-system) (arguments (list @@ -12788,14 +13188,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.64.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9")))) + "0p8cd4r3c8va5gybs1vlm3kn7jcg1xg529hvvg27fybb3g91nvqg")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -13145,14 +13545,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg")))) + "16316a5pgyl5rppyviibf6z3k3m7xmvqyylf1kxdpg0avs6dk8w7")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -13736,23 +14136,20 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n")))) + "0rgqlqasil75b03c8c4nyg71ybysrsbqb0bwk6hbnaw8rljxdmi5")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-bh - r-rcpp - r-rcpparmadillo - r-rcppparallel r-rhdf5lib r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") @@ -14842,6 +15239,47 @@ be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) +(define-public r-tilingarray + (package + (name "r-tilingarray") + (version "1.76.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tilingArray" version)) + (sha256 + (base32 + "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd")))) + (properties `((upstream-name . "tilingArray"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-genefilter + r-pixmap + r-rcolorbrewer + r-strucchange + r-vsn)) + (home-page "https://bioconductor.org/packages/tilingArray") + (synopsis "Transcript mapping with high-density oligonucleotide tiling arrays") + (description + "The package provides functionality that can be useful for the analysis +of the high-density tiling microarray data (such as from Affymetrix genechips) +or for measuring the transcript abundance and the architecture. The main +functionalities of the package are: + +@enumerate +@item the class segmentation for representing partitionings of a linear series + of data; +@item the function segment for fitting piecewise constant models using a + dynamic programming algorithm that is both fast and exact; +@item the function @code{confint} for calculating confidence intervals using + the @code{strucchange} package; +@item the function @code{plotAlongChrom} for generating pretty plots; +@item the function @code{normalizeByReference} for probe-sequence dependent + response adjustment from a (set of) reference hybridizations. +@end enumerate") + (license license:artistic2.0))) + (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") @@ -14992,14 +15430,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.28.1") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0ypw3ckaf4qll83rl2bjzfc7g2m4v0n2mq645ppyfga8wv8kwssy")))) + "1ii4r0c76b7rnisy4qba2cp5686j73s6b3s6pj66w91wq65dykpd")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -16548,14 +16986,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.60.1") + (version "1.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1")))) + "0ikxikmz9dy09g726q1wygymm6z2imlgfiizkgh1cl4s0m35fbbd")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -16598,14 +17036,14 @@ S4Vectors package itself.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.71") + (version "1.72-1") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91")))) + "1p3zsl5r6l5r6ylnrxmbxjpim5qgmncgdjcgn5j69rzk3rv85gqx")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -16896,6 +17334,26 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +(define-public r-beadarraysnp + (package + (name "r-beadarraysnp") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beadarraySNP" version)) + (sha256 + (base32 "06hy89pclbyxjw5yf5i9bc3wr789b9pmhd9sdchgljlijs9vcj6g")))) + (properties `((upstream-name . "beadarraySNP"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-quantsmooth)) + (home-page "https://bioconductor.org/packages/beadarraySNP") + (synopsis "Normalization and reporting of Illumina SNP bead arrays") + (description + "This package is importing data from Illumina SNP experiments and it +performs copy number calculations and reports.") + (license license:gpl2))) + ;; This package includes files that have been taken from kentutils. Some ;; parts of kentutils are not released under a free license, but this package ;; only uses files that are also found in the free parts of kentutils. @@ -17166,14 +17624,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.3") + (version "1.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i")))) + "04257gl995r575md1n3h2gy502yi6c8x3352l96mib7rdv4yg53f")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -17246,14 +17704,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.26.1") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p")))) + "0r80k4dsk609l9ha1jl64yhpwnf0x37i28k9largqsffsl6hw0fy")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -17765,14 +18223,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.42.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9")))) + "01qs60sdh7c8cxkv3qbfcfwpjhab88j872va50fi95xsqnmj5isa")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -17934,14 +18392,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.7-1") + (version "2.7-3") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr")))) + "02qmp3ky671fkpjq1vcb083zzvfn5gkf69rhvdlvg7siy5wrjll3")))) (build-system r-build-system) (inputs (list gsl)) @@ -18027,6 +18485,34 @@ integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+))) +(define-public r-snapcgh + (package + (name "r-snapcgh") + (version "1.68.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "snapCGH" version)) + (sha256 + (base32 + "1zxvl8mkby7yb5kppddag6k9w78d1fm6adx52h4cgrfckn28w64q")))) + (properties `((upstream-name . "snapCGH"))) + (build-system r-build-system) + (propagated-inputs + (list r-acgh + r-cluster + r-dnacopy + r-glad + r-limma + r-tilingarray)) + (home-page "https://bioconductor.org/packages/snapCGH") + (synopsis "Segmentation, normalisation and processing of the aCGH data") + (description + "This package provides methods for segmenting, normalising and processing +aCGH data. snapCGH also includes plotting functions for visualising raw and +segmented data for individual and multiple arrays.") + ;; Expanded from GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-snpstats (package (name "r-snpstats") @@ -19240,14 +19726,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna")))) + "15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |