diff options
-rw-r--r-- | gnu/packages/bioconductor.scm | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3692bb94af..b323541f82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2293,6 +2293,46 @@ reproducible gene expression signatures capable of accurately distinguishing tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-baalchip + (package + (name "r-baalchip") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BaalChIP" version)) + (sha256 + (base32 + "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q")))) + (properties `((upstream-name . "BaalChIP"))) + (build-system r-build-system) + (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl + (propagated-inputs + (list r-coda + r-doby + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-reshape2 + r-rsamtools + r-scales)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BaalChIP") + (synopsis + "Analysis of allele-specific transcription factor binding in cancer genomes") + (description + "This package offers functions to process multiple @code{ChIP-seq BAM} +files and detect allele-specific events. It computes allele counts at +individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality +control) steps to remove problematic variants, and utilizes a Bayesian +framework to identify statistically significant allele-specific events. +BaalChIP is able to account for copy number differences between the two +alleles, a known phenotypical feature of cancer samples.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") |