diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 72 |
1 files changed, 70 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ff159638b3..a1f7b2d2a8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -590,6 +590,35 @@ data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" track. The database is exposed as a @code{TxDb} object.") (license license:artistic2.0))) +(define-public r-txdb-hsapiens-ucsc-hg38-knowngene + (package + (name "r-txdb-hsapiens-ucsc-hg38-knowngene") + (version "3.4.6") + (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://bioconductor.org/packages/" + "release/data/annotation/src/contrib" + "/TxDb.Hsapiens.UCSC.hg38.knownGene_" + version ".tar.gz")) + (sha256 + (base32 + "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) + (properties + `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures))) + (home-page + "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") + (synopsis "Annotation package for human genome in TxDb format") + (description + "This package provides an annotation database of Homo sapiens genome +data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" +track. The database is exposed as a @code{TxDb} object.") + (license license:artistic2.0))) + (define-public r-txdb-mmusculus-ucsc-mm9-knowngene (package (name "r-txdb-mmusculus-ucsc-mm9-knowngene") @@ -4438,14 +4467,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "1y3zqvk1vbcb10r1myh6f5yzjvf7bhwhpiq78bs1k6spli4bzj0q")))) + "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (native-inputs @@ -4677,3 +4706,42 @@ Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.") (license license:cecill))) + +(define-public r-annotatr + (package + (name "r-annotatr") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "annotatr" version)) + (sha256 + (base32 + "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-readr" ,r-readr) + ("r-regioner" ,r-regioner) + ("r-reshape2" ,r-reshape2) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/annotatr/") + (synopsis "Annotation of genomic regions to genomic annotations") + (description + "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, +differentially methylated CpGs or regions, SNPs, etc.) it is often of interest +to investigate the intersecting genomic annotations. Such annotations include +those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), +CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as +enhancers. The annotatr package provides an easy way to summarize and +visualize the intersection of genomic sites/regions with genomic +annotations.") + (license license:gpl3))) |