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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 259 |
1 files changed, 259 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 09581d9fde..76ff773ef1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -23,6 +23,8 @@ #:use-module (guix download) #:use-module (guix build-system r) #:use-module (gnu packages) + #:use-module (gnu packages cran) + #:use-module (gnu packages compression) #:use-module (gnu packages statistics) #:use-module (gnu packages bioinformatics)) @@ -70,3 +72,260 @@ the Human Protein Atlas project.") customizable permutation tests to assess the association between genomic region sets and other genomic features.") (license license:artistic2.0))) + +(define-public r-diffbind + (package + (name "r-diffbind") + (version "2.6.6") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DiffBind" version)) + (sha256 + (base32 + "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp")))) + (properties `((upstream-name . "DiffBind"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-amap" ,r-amap) + ("r-biocparallel" ,r-biocparallel) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-genomicalignments" ,r-genomicalignments) + ("r-ggrepel" ,r-ggrepel) + ("r-gplots" ,r-gplots) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-rcolorbrewer" , r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-systempiper" ,r-systempiper) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "http://bioconductor.org/packages/DiffBind") + (synopsis "Differential binding analysis of ChIP-Seq peak data") + (description + "This package computes differentially bound sites from multiple +ChIP-seq experiments using affinity (quantitative) data. Also enables +occupancy (overlap) analysis and plotting functions.") + (license license:artistic2.0))) + +(define-public r-ripseeker + (package + (name "r-ripseeker") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RIPSeeker" version)) + (sha256 + (base32 + "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y")))) + (properties `((upstream-name . "RIPSeeker"))) + (build-system r-build-system) + (propagated-inputs + `(("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-genomicranges" ,r-genomicranges) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rsamtools" ,r-rsamtools) + ("r-genomicalignments" ,r-genomicalignments) + ("r-rtracklayer" ,r-rtracklayer))) + (home-page "http://bioconductor.org/packages/RIPSeeker") + (synopsis + "Identifying protein-associated transcripts from RIP-seq experiments") + (description + "This package infers and discriminates RIP peaks from RIP-seq alignments +using two-state HMM with negative binomial emission probability. While +RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides +a suite of bioinformatics tools integrated within this self-contained software +package comprehensively addressing issues ranging from post-alignments +processing to visualization and annotation.") + (license license:gpl2))) + +(define-public r-multtest + (package + (name "r-multtest") + (version "2.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "multtest" version)) + (sha256 + (base32 + "0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j")))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biobase" ,r-biobase) + ("r-mass" ,r-mass))) + (home-page "http://bioconductor.org/packages/multtest") + (synopsis "Resampling-based multiple hypothesis testing") + (description + "This package can do non-parametric bootstrap and permutation +resampling-based multiple testing procedures (including empirical Bayes +methods) for controlling the family-wise error rate (FWER), generalized +family-wise error rate (gFWER), tail probability of the proportion of +false positives (TPPFP), and false discovery rate (FDR). Several choices +of bootstrap-based null distribution are implemented (centered, centered +and scaled, quantile-transformed). Single-step and step-wise methods are +available. Tests based on a variety of T- and F-statistics (including +T-statistics based on regression parameters from linear and survival models +as well as those based on correlation parameters) are included. When probing +hypotheses with T-statistics, users may also select a potentially faster null +distribution which is multivariate normal with mean zero and variance +covariance matrix derived from the vector influence function. Results are +reported in terms of adjusted P-values, confidence regions and test statistic +cutoffs. The procedures are directly applicable to identifying differentially +expressed genes in DNA microarray experiments.") + (license license:lgpl3))) + +(define-public r-chippeakanno + (package + (name "r-chippeakanno") + (version "3.12.7") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPpeakAnno" version)) + (sha256 + (base32 + "1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04")))) + (properties `((upstream-name . "ChIPpeakAnno"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) + ("r-biomart" ,r-biomart) + ("r-bsgenome" ,r-bsgenome) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-matrixstats" ,r-matrixstats) + ("r-annotationdbi" ,r-annotationdbi) + ("r-limma" ,r-limma) + ("r-multtest" ,r-multtest) + ("r-rbgl" ,r-rbgl) + ("r-graph" ,r-graph) + ("r-biocinstaller" ,r-biocinstaller) + ("r-regioner" ,r-regioner) + ("r-dbi" ,r-dbi) + ("r-ensembldb" ,r-ensembldb) + ("r-biobase" ,r-biobase) + ("r-seqinr" ,r-seqinr) + ("r-idr" ,r-idr) + ("r-genomicalignments" ,r-genomicalignments) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rsamtools" ,r-rsamtools) + ("r-venndiagram" ,r-venndiagram))) + (home-page "http://bioconductor.org/packages/ChIPpeakAnno") + (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") + (description + "The package includes functions to retrieve the sequences around the peak, +obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or +custom features such as most conserved elements and other transcription factor +binding sites supplied by users. Starting 2.0.5, new functions have been added +for finding the peaks with bi-directional promoters with summary statistics +(peaksNearBDP), for summarizing the occurrence of motifs in peaks +(summarizePatternInPeaks) and for adding other IDs to annotated peaks or +enrichedGO (addGeneIDs).") + (license license:gpl2+))) + +(define-public r-marray + (package + (name "r-marray") + (version "1.56.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "marray" version)) + (sha256 + (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limma" ,r-limma))) + (home-page "http://bioconductor.org/packages/marray") + (synopsis "Exploratory analysis for two-color spotted microarray data") + (description "This package contains class definitions for two-color spotted +microarray data. It also includes fuctions for data input, diagnostic plots, +normalization and quality checking.") + (license license:lgpl2.0+))) + +(define-public r-cghbase + (package + (name "r-cghbase") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CGHbase" version)) + (sha256 + (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm")))) + (properties `((upstream-name . "CGHbase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-marray" ,r-marray))) + (home-page "http://bioconductor.org/packages/CGHbase") + (synopsis "Base functions and classes for arrayCGH data analysis") + (description "This package contains functions and classes that are needed by +the @code{arrayCGH} packages.") + (license license:gpl2+))) + +(define-public r-cghcall + (package + (name "r-cghcall") + (version "2.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CGHcall" version)) + (sha256 + (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch")))) + (properties `((upstream-name . "CGHcall"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-cghbase" ,r-cghbase) + ("r-impute" ,r-impute) + ("r-dnacopy" ,r-dnacopy) + ("r-snowfall" ,r-snowfall))) + (home-page "http://bioconductor.org/packages/CGHcall") + (synopsis "Base functions and classes for arrayCGH data analysis") + (description "This package contains functions and classes that are needed by +@code{arrayCGH} packages.") + (license license:gpl2+))) + +(define-public r-qdnaseq + (package + (name "r-qdnaseq") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "QDNAseq" version)) + (sha256 + (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy")))) + (properties `((upstream-name . "QDNAseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-cghbase" ,r-cghbase) + ("r-cghcall" ,r-cghcall) + ("r-dnacopy" ,r-dnacopy) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-r-utils" ,r-r-utils) + ("r-rsamtools" ,r-rsamtools))) + (home-page "http://bioconductor.org/packages/QDNAseq") + (synopsis "Quantitative DNA sequencing for chromosomal aberrations") + (description "The genome is divided into non-overlapping fixed-sized bins, +number of sequence reads in each counted, adjusted with a simultaneous +two-dimensional loess correction for sequence mappability and GC content, and +filtered to remove spurious regions in the genome. Downstream steps of +segmentation and calling are also implemented via packages DNAcopy and CGHcall, +respectively.") + (license license:gpl2+))) |