diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 615 |
1 files changed, 598 insertions, 17 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 37cd51d16c..7ca6788dd8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -50,21 +50,14 @@ (version "1.4.0") (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 "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Celegans.UCSC.ce6_" - version ".tar.gz")) + (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" + version 'annotation)) (sha256 (base32 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) (properties `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (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 `(("r-bsgenome" ,r-bsgenome))) (home-page @@ -817,6 +810,28 @@ annotations.") Disease Ontology.") (license license:artistic2.0))) +(define-public r-pfam-db + (package + (name "r-pfam-db") + (version "3.8.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "PFAM.db" version 'annotation)) + (sha256 + (base32 + "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) + (properties `((upstream-name . "PFAM.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/PFAM.db") + (synopsis "Set of protein ID mappings for PFAM") + (description + "This package provides a set of protein ID mappings for PFAM, assembled +using data from public repositories.") + (license license:artistic2.0))) + ;;; Experiment data @@ -942,6 +957,29 @@ jointly normalized data that are available here. The data are presented in the form of an @code{exprSet} object.") (license license:artistic2.0))) +(define-public r-affydata + (package + (name "r-affydata") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affydata" version 'experiment)) + (sha256 + (base32 + "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) + (properties `((upstream-name . "affydata"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy))) + (home-page "https://bioconductor.org/packages/affydata/") + (synopsis "Affymetrix data for demonstration purposes") + (description + "This package provides example datasets that represent 'real world +examples' of Affymetrix data, unlike the artificial examples included in the +package @code{affy}.") + (license license:gpl2+))) + ;;; Packages @@ -965,6 +1003,147 @@ the form of an @code{exprSet} object.") packages.") (license license:artistic2.0))) +(define-public r-affycomp + (package + (name "r-affycomp") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affycomp" version)) + (sha256 + (base32 + "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n")))) + (properties `((upstream-name . "affycomp"))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/affycomp/") + (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") + (description + "The package contains functions that can be used to compare expression +measures for Affymetrix Oligonucleotide Arrays.") + (license license:gpl2+))) + +(define-public r-affycompatible + (package + (name "r-affycompatible") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AffyCompatible" version)) + (sha256 + (base32 + "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs")))) + (properties + `((upstream-name . "AffyCompatible"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml))) + (home-page "https://bioconductor.org/packages/AffyCompatible/") + (synopsis "Work with Affymetrix GeneChip files") + (description + "This package provides an interface to Affymetrix chip annotation and +sample attribute files. The package allows an easy way for users to download +and manage local data bases of Affynmetrix NetAffx annotation files. It also +provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip +Command Console} (AGCC)-compatible sample annotation files.") + (license license:artistic2.0))) + +(define-public r-affycontam + (package + (name "r-affycontam") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyContam" version)) + (sha256 + (base32 + "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp")))) + (properties `((upstream-name . "affyContam"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-affydata" ,r-affydata) + ("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/affyContam/") + (synopsis "Structured corruption of Affymetrix CEL file data") + (description + "Microarray quality assessment is a major concern of microarray analysts. +This package provides some simple approaches to in silico creation of quality +problems in CEL-level data to help evaluate performance of quality metrics.") + (license license:artistic2.0))) + +(define-public r-affycoretools + (package + (name "r-affycoretools") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affycoretools" version)) + (sha256 + (base32 + "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s")))) + (properties `((upstream-name . "affycoretools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-edger" ,r-edger) + ("r-gcrma" ,r-gcrma) + ("r-ggplot2" ,r-ggplot2) + ("r-gostats" ,r-gostats) + ("r-gplots" ,r-gplots) + ("r-hwriter" ,r-hwriter) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma) + ("r-oligoclasses" ,r-oligoclasses) + ("r-reportingtools" ,r-reportingtools) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/affycoretools/") + (synopsis "Functions for analyses with Affymetrix GeneChips") + (description + "This package provides various wrapper functions that have been written +to streamline the more common analyses that a Biostatistician might see.") + (license license:artistic2.0))) + +(define-public r-affxparser + (package + (name "r-affxparser") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affxparser" version)) + (sha256 + (base32 + "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33")))) + (properties `((upstream-name . "affxparser"))) + (build-system r-build-system) + (home-page "https://github.com/HenrikBengtsson/affxparser") + (synopsis "Affymetrix File Parsing SDK") + (description + "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, +BAR). It provides methods for fast and memory efficient parsing of Affymetrix +files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files +are supported. Currently, there are methods for reading @dfn{chip definition +file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read +either in full or in part. For example, probe signals from a few probesets +can be extracted very quickly from a set of CEL files into a convenient list +structure.") + ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is + ;; under LGPLv2+. + (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) + (define-public r-annotate (package (name "r-annotate") @@ -1013,14 +1192,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.16.2") + (version "1.16.4") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q")))) + "0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -1039,6 +1218,54 @@ customizable permutation tests to assess the association between genomic region sets and other genomic features.") (license license:artistic2.0))) +(define-public r-reportingtools + (package + (name "r-reportingtools") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ReportingTools" version)) + (sha256 + (base32 + "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc")))) + (properties + `((upstream-name . "ReportingTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-category" ,r-category) + ("r-deseq2" ,r-deseq2) + ("r-edger" ,r-edger) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-gostats" ,r-gostats) + ("r-gseabase" ,r-gseabase) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-knitr" ,r-knitr) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma) + ("r-pfam-db" ,r-pfam-db) + ("r-r-utils" ,r-r-utils) + ("r-xml" ,r-xml))) + (home-page "https://bioconductor.org/packages/ReportingTools/") + (synopsis "Tools for making reports in various formats") + (description + "The ReportingTools package enables users to easily display reports of +analysis results generated from sources such as microarray and sequencing +data. The package allows users to create HTML pages that may be viewed on a +web browser, or in other formats. Users can generate tables with sortable and +filterable columns, make and display plots, and link table entries to other +data sources such as NCBI or larger plots within the HTML page. Using the +package, users can also produce a table of contents page to link various +reports together for a particular project that can be viewed in a web +browser.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") @@ -1064,6 +1291,75 @@ region sets and other genomic features.") "This package provides functions for plotting genomic data.") (license license:artistic2.0))) +(define-public r-oligoclasses + (package + (name "r-oligoclasses") + (version "1.46.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "oligoClasses" version)) + (sha256 + (base32 + "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72")))) + (properties `((upstream-name . "oligoClasses"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-ff" ,r-ff) + ("r-foreach" ,r-foreach) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/oligoClasses/") + (synopsis "Classes for high-throughput arrays") + (description + "This package contains class definitions, validity checks, and +initialization methods for classes used by the @code{oligo} and @code{crlmm} +packages.") + (license license:gpl2+))) + +(define-public r-oligo + (package + (name "r-oligo") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "oligo" version)) + (sha256 + (base32 + "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df")))) + (properties `((upstream-name . "oligo"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-affxparser" ,r-affxparser) + ("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-ff" ,r-ff) + ("r-oligoclasses" ,r-oligoclasses) + ("r-preprocesscore" ,r-preprocesscore) + ("r-rsqlite" ,r-rsqlite) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/oligo/") + (synopsis "Preprocessing tools for oligonucleotide arrays") + (description + "This package provides a package to analyze oligonucleotide +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-qvalue (package (name "r-qvalue") @@ -3895,14 +4191,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y")))) + "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) @@ -4888,14 +5184,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "1.34.6") + (version "1.34.7") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550")))) + "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -5047,14 +5343,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.8.2") + (version "6.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0issfrhsgc102sr33q9v6w6jrrd32plig7szd1nm0n4r3yn4y2fc")))) + "0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -5466,3 +5762,288 @@ with multiple R processes supported by the package @code{parallel}.") "This package provides methods for working with Illumina arrays using the @code{gdsfmt} package.") (license license:gpl3))) + +(define-public r-seqbias + (package + (name "r-seqbias") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "seqbias" version)) + (sha256 + (base32 + "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw")))) + (properties `((upstream-name . "seqbias"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-rhtslib" ,r-rhtslib))) + (inputs + `(("zlib" ,zlib))) ; This comes from rhtslib. + (home-page "https://bioconductor.org/packages/seqbias/") + (synopsis "Estimation of per-position bias in high-throughput sequencing data") + (description + "This package implements a model of per-position sequencing bias in +high-throughput sequencing data using a simple Bayesian network, the structure +and parameters of which are trained on a set of aligned reads and a reference +genome sequence.") + (license license:lgpl3))) + +(define-public r-reqon + (package + (name "r-reqon") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ReQON" version)) + (sha256 + (base32 + "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a")))) + (properties `((upstream-name . "ReQON"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rjava" ,r-rjava) + ("r-rsamtools" ,r-rsamtools) + ("r-seqbias" ,r-seqbias))) + (home-page "https://bioconductor.org/packages/ReQON/") + (synopsis "Recalibrating quality of nucleotides") + (description + "This package provides an implementation of an algorithm for +recalibrating the base quality scores for aligned sequencing data in BAM +format.") + (license license:gpl2))) + +(define-public r-wavcluster + (package + (name "r-wavcluster") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "wavClusteR" version)) + (sha256 + (base32 + "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2")))) + (properties `((upstream-name . "wavClusteR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-foreach" ,r-foreach) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-mclust" ,r-mclust) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr) + ("r-stringr" ,r-stringr) + ("r-wmtsa" ,r-wmtsa))) + (home-page "https://bioconductor.org/packages/wavClusteR/") + (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") + (description + "This package provides an integrated pipeline for the analysis of +PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from +sequencing errors, SNPs and additional non-experimental sources by a non- +parametric mixture model. The protein binding sites (clusters) are then +resolved at high resolution and cluster statistics are estimated using a +rigorous Bayesian framework. Post-processing of the results, data export for +UCSC genome browser visualization and motif search analysis are provided. In +addition, the package allows to integrate RNA-Seq data to estimate the False +Discovery Rate of cluster detection. Key functions support parallel multicore +computing. While wavClusteR was designed for PAR-CLIP data analysis, it can +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-timeseriesexperiment + (package + (name "r-timeseriesexperiment") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TimeSeriesExperiment" version)) + (sha256 + (base32 + "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y")))) + (properties + `((upstream-name . "TimeSeriesExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-edger" ,r-edger) + ("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc) + ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) + ("r-proxy" ,r-proxy) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-vegan" ,r-vegan) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") + (synopsis "Analysis for short time-series data") + (description + "This package is a visualization and analysis toolbox for short time +course data which includes dimensionality reduction, clustering, two-sample +differential expression testing and gene ranking techniques. The package also +provides methods for retrieving enriched pathways.") + (license license:lgpl3+))) + +(define-public r-variantfiltering + (package + (name "r-variantfiltering") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "VariantFiltering" version)) + (sha256 + (base32 + "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17")))) + (properties + `((upstream-name . "VariantFiltering"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-dt" ,r-dt) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-genomicscores" ,r-genomicscores) + ("r-graph" ,r-graph) + ("r-gviz" ,r-gviz) + ("r-iranges" ,r-iranges) + ("r-rbgl" ,r-rbgl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-shinyjs" ,r-shinyjs) + ("r-shinythemes" ,r-shinythemes) + ("r-shinytree" ,r-shinytree) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation) + ("r-xvector" ,r-xvector))) + (home-page "https://github.com/rcastelo/VariantFiltering") + (synopsis "Filtering of coding and non-coding genetic variants") + (description + "Filter genetic variants using different criteria such as inheritance +model, amino acid change consequence, minor allele frequencies across human +populations, splice site strength, conservation, etc.") + (license license:artistic2.0))) + +(define-public r-genomegraphs + (package + (name "r-genomegraphs") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeGraphs" version)) + (sha256 + (base32 + "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd")))) + (properties `((upstream-name . "GenomeGraphs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biomart" ,r-biomart))) + (home-page "https://bioconductor.org/packages/GenomeGraphs/") + (synopsis "Plotting genomic information from Ensembl") + (description + "Genomic data analyses requires integrated visualization of known genomic +information and new experimental data. GenomeGraphs uses the biomaRt package +to perform live annotation queries to Ensembl and translates this to e.g. +gene/transcript structures in viewports of the grid graphics package. This +results in genomic information plotted together with your data. Another +strength of GenomeGraphs is to plot different data types such as array CGH, +gene expression, sequencing and other data, together in one plot using the +same genome coordinate system.") + (license license:artistic2.0))) + +(define-public r-wavetiling + (package + (name "r-wavetiling") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "waveTiling" version)) + (sha256 + (base32 + "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir")))) + (properties `((upstream-name . "waveTiling"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-biostrings" ,r-biostrings) + ("r-genomegraphs" ,r-genomegraphs) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-oligo" ,r-oligo) + ("r-oligoclasses" ,r-oligoclasses) + ("r-preprocesscore" ,r-preprocesscore) + ("r-waveslim" ,r-waveslim))) + (home-page "https://r-forge.r-project.org/projects/wavetiling/") + (synopsis "Wavelet-based models for tiling array transcriptome analysis") + (description + "This package is designed to conduct transcriptome analysis for tiling +arrays based on fast wavelet-based functional models.") + (license license:gpl2+))) + +(define-public r-variancepartition + (package + (name "r-variancepartition") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "variancePartition" version)) + (sha256 + (base32 + "1ycapwb2mq57xibrzzjz9zwxqz4nwz9f3n5gskhlr5vcs7irkjd6")))) + (properties + `((upstream-name . "variancePartition"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-colorramps" ,r-colorramps) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-iterators" ,r-iterators) + ("r-limma" ,r-limma) + ("r-lme4" ,r-lme4) + ("r-lmertest" ,r-lmertest) + ("r-mass" ,r-mass) + ("r-pbkrtest" ,r-pbkrtest) + ("r-progress" ,r-progress) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales))) + (home-page "https://bioconductor.org/packages/variancePartition/") + (synopsis "Analyze variation in gene expression experiments") + (description + "This is a package providing tools to quantify and interpret multiple +sources of biological and technical variation in gene expression experiments. +It uses a linear mixed model to quantify variation in gene expression +attributable to individual, tissue, time point, or technical variables. The +package includes dream differential expression analysis for repeated +measures.") + (license license:gpl2+))) |