diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 278 |
1 files changed, 277 insertions, 1 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68d8e5b574..b4be8aee15 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> ;;; @@ -493,6 +493,30 @@ annotations for the genome of the model mouse Mus musculus.") by UCSC (hg19, February 2009) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-hsapiens-ucsc-hg38 + (package + (name "r-bsgenome-hsapiens-ucsc-hg38") + (version "1.4.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" + version 'annotation)) + (sha256 + (base32 + "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) + (properties + `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome))) + (home-page + "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") + (synopsis "Full genome sequences for Homo sapiens") + (description + "This package provides full genome sequences for Homo sapiens (Human) +as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-ensdb-hsapiens-v75 (package (name "r-ensdb-hsapiens-v75") @@ -718,6 +742,30 @@ annotations.") "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +(define-public r-ideoviz + (package + (name "r-ideoviz") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "IdeoViz" version)) + (sha256 + (base32 + "0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-iranges" ,r-iranges) + ("r-genomicranges" ,r-genomicranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer) + ("r-genomeinfodb" ,r-genomeinfodb))) + (home-page "https://bioconductor.org/packages/IdeoViz/") + (synopsis "Plots data along a chromosomal ideogram") + (description "This package provides functions to plot data associated with +arbitrary genomic intervals along chromosomal ideogram.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs @@ -811,6 +859,32 @@ performing parallel computations on multicore machines.") Disease Ontology.") (license license:artistic2.0))) +(define-public r-pasilla + (package + (name "r-pasilla") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (string-append + "http://bioconductor.org/packages/release/data/experiment" + "/src/contrib/pasilla_" version ".tar.gz")) + (sha256 + (base32 + "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocstyle" ,r-biocstyle) + ("r-dexseq" ,r-dexseq) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown))) + (home-page "https://www.bioconductor.org/packages/pasilla/") + (synopsis "Data package with per-exon and per-gene read counts") + (description "This package provides per-exon and per-gene read counts +computed for selected genes from RNA-seq data that were presented in the +article 'Conservation of an RNA regulatory map between Drosophila and mammals' +by Brooks et al., Genome Research 2011.") + (license license:lgpl2.1+))) + (define-public r-pfam-db (package (name "r-pfam-db") @@ -995,6 +1069,63 @@ examples' of Affymetrix data, unlike the artificial examples included in the package @code{affy}.") (license license:gpl2+))) +(define-public r-coverageview + (package + (name "r-coverageview") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CoverageView" version)) + (sha256 + (base32 + "0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf")))) + (build-system r-build-system) + (propagated-inputs + `(("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-genomicranges" ,r-genomicranges) + ("r-genomicalignments" ,r-genomicalignments) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rsamtools" ,r-rsamtools))) + (home-page "https://bioconductor.org/packages/CoverageView/") + (synopsis "Coverage visualization package for R") + (description "This package provides a framework for the visualization of +genome coverage profiles. It can be used for ChIP-seq experiments, but it can +be also used for genome-wide nucleosome positioning experiments or other +experiment types where it is important to have a framework in order to inspect +how the coverage distributed across the genome.") + (license license:artistic2.0))) + +(define-public r-cummerbund + (package + (name "r-cummerbund") + (version "2.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "cummeRbund" version)) + (sha256 + (base32 + "1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fastcluster", r-fastcluster) + ("r-ggplot2" ,r-ggplot2) + ("r-gviz" ,r-gviz) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/cummeRbund/") + (synopsis "Analyze Cufflinks high-throughput sequencing data") + (description "This package allows for persistent storage, access, +exploration, and manipulation of Cufflinks high-throughput sequencing +data. In addition, provides numerous plotting functions for commonly +used visualizations.") + (license license:artistic2.0))) + (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") @@ -2533,6 +2664,41 @@ and regression inferences from RNA-sequencing data.") gene and isoform level using RNA-seq data") (license license:artistic2.0))) +(define-public r-karyoploter + (package + (name "r-karyoploter") + (version "1.12.4") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "karyoploteR" version)) + (sha256 + (base32 + "03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-regioner" ,r-regioner) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-memoise" ,r-memoise) + ("r-rtracklayer" ,r-rtracklayer) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-s4vectors" ,r-s4vectors) + ("r-biovizbase" ,r-biovizbase) + ("r-digest" ,r-digest) + ("r-bezier" ,r-bezier) + ("r-bamsignals" ,r-bamsignals) + ("r-annotationdbi" ,r-annotationdbi) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/karyoploteR/") + (synopsis "Plot customizable linear genomes displaying arbitrary data") + (description "This package creates karyotype plots of arbitrary genomes and +offers a complete set of functions to plot arbitrary data on them. It mimicks +many R base graphics functions coupling them with a coordinate change function +automatically mapping the chromosome and data coordinates into the plot +coordinates.") + (license license:artistic2.0))) + (define-public r-lpsymphony (package (name "r-lpsymphony") @@ -3972,6 +4138,78 @@ database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.") (license license:gpl2))) +(define-public r-motifdb + (package + (name "r-motifdb") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "MotifDb" version)) + (sha256 + (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc")))) + (properties `((upstream-name . "MotifDb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-iranges" ,r-iranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-splitstackshape" ,r-splitstackshape))) + (home-page "https://www.bioconductor.org/packages/MotifDb/") + (synopsis "Annotated collection of protein-DNA binding sequence motifs") + (description "This package provides more than 2000 annotated position +frequency matrices from nine public sources, for multiple organisms.") + (license license:artistic2.0))) + +(define-public r-motifbreakr + (package + (name "r-motifbreakr") + (version "2.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "motifbreakR" version)) + (sha256 + (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n")))) + (properties `((upstream-name . "motifbreakR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-grimport" ,r-grimport) + ("r-stringr" ,r-stringr) + ("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-rtracklayer" ,r-rtracklayer) + ("r-variantannotation" ,r-variantannotation) + ("r-biocparallel" ,r-biocparallel) + ("r-motifstack" ,r-motifstack) + ("r-gviz" ,r-gviz) + ("r-matrixstats" ,r-matrixstats) + ("r-tfmpvalue" ,r-tfmpvalue) + ("r-motifdb" ,r-motifdb))) + (home-page "https://www.bioconductor.org/packages/motifbreakR/") + (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") + (description "This package allows biologists to judge in the first place +whether the sequence surrounding the polymorphism is a good match, and in +the second place how much information is gained or lost in one allele of +the polymorphism relative to another. This package gives a choice of +algorithms for interrogation of genomes with motifs from public sources: +@enumerate +@item a weighted-sum probability matrix; +@item log-probabilities; +@item weighted by relative entropy. +@end enumerate + +This package can predict effects for novel or previously described variants in +public databases, making it suitable for tasks beyond the scope of its original +design. Lastly, it can be used to interrogate any genome curated within +Bioconductor.") + (license license:gpl2+))) + (define-public r-motifstack (package (name "r-motifstack") @@ -6368,6 +6606,44 @@ and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) +(define-public r-snplocs-hsapiens-dbsnp144-grch37 + (package + (name "r-snplocs-hsapiens-dbsnp144-grch37") + (version "0.99.20") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" + version 'annotation)) + (sha256 + (base32 + "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) + (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-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-bsgenome" ,r-bsgenome) + ("r-biostrings" ,r-biostrings))) + (home-page + "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") + (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") + (description "This package provides SNP locations and alleles for Homo +sapiens extracted from NCBI dbSNP Build 144. The source data files used for +this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped +to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a +patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, +X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for +the mitochondrion chromosome. Therefore, the SNPs in this package can be +injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the +correct position but this injection will exclude chrM (i.e. nothing will be +injected in that sequence).") + (license license:artistic2.0))) + (define-public r-reqon (package (name "r-reqon") |