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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1401053570..bae472c8ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11608,6 +11608,35 @@ enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.") (license license:gpl3))) +(define-public r-ace + (package + (name "r-ace") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ACE" version)) + (sha256 + (base32 + "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6")))) + (properties `((upstream-name . "ACE"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tgac-vumc/ACE") + (synopsis + "Absolute copy number estimation from low-coverage whole genome sequencing") + (description + "This package uses segmented copy number data to estimate tumor cell +percentage and produce copy number plots displaying absolute copy numbers. For +this it uses segmented data from the @code{QDNAseq} package, which in turn uses +a number of dependencies to turn mapped reads into segmented data. @code{ACE} +will run @code{QDNAseq} or use its output rds-file of segmented data. It will +subsequently run through all samples in the object(s), for which it will create +individual subdirectories. For each sample, it will calculate how well the +segments fit (the relative error) to integer copy numbers for each percentage +of @dfn{tumor cells} (cells with divergent segments).") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs |