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(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) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (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 + "The package offers functions to process multiple @code{ChIP-seq BAM} files +and detect allele-specific events. 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. @code{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")