diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 308 |
1 files changed, 306 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed35b4c61a..a6a8216ccb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -24,10 +24,11 @@ #: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 @@ -61,6 +62,111 @@ melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings 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-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-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") @@ -371,3 +477,201 @@ 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+))) + +(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))) + +(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+))) + +(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))) + +(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))) + +(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))) + +(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))) |