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| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2022-10-27 00:38:09 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-10-27 13:54:18 +0200 |
| commit | 4b9fa56cadf7442addf22451fc4a7d5a0d34879e (patch) | |
| tree | 753e84b557443d4d0ca9256f350fe34b0565ab86 | |
| parent | 8e6a9b23d07a3f0cf6f7498ed6d054da8a126a8d (diff) | |
gnu: Add r-baalchip.
* gnu/packages/bioconductor.scm (r-baalchip): New variable.
| -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") |