diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7cf6811d52..9a00baa89b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -185,3 +185,53 @@ 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+))) |