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| author | Ricardo Wurmus <rekado@elephly.net> | 2020-06-23 13:41:36 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2020-06-23 13:43:12 +0200 |
| commit | 755733a3fee60097735ac85a388b582b30e68b88 (patch) | |
| tree | 01a4007f6d8c03bc62ea2624356dc477a2355246 /gnu/packages | |
| parent | c261a7b39ab8f5d46299205e5421cb46aae5634e (diff) | |
| download | guix-755733a3fee60097735ac85a388b582b30e68b88.tar.gz | |
gnu: Add r-fourcseq.
* gnu/packages/cran.scm (r-fourcseq): New variable. Co-authored-by: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/cran.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ac246bd123..e81d11e6e5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22230,3 +22230,47 @@ inferring an appropriate positioning method.") Try a demo of the LSD by running @code{demotour()}.") ;; Either version (license (list license:gpl2 license:gpl3)))) + +(define-public r-fourcseq + (package + (name "r-fourcseq") + (version "1.21.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FourCSeq" version)) + (sha256 + (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x")))) + (properties `((upstream-name . "FourCSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-fda" ,r-fda) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-gtools" ,r-gtools) + ("r-lsd" ,r-lsd) + ("r-matrix" ,r-matrix) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") + (synopsis "Analysis of multiplexed 4C sequencing data") + (description + "This package is an R package dedicated to the analysis of (multiplexed) +4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific +interactions between DNA elements and identify differential interactions +between conditions. The statistical analysis in R starts with individual bam +files for each sample as inputs. To obtain these files, the package contains +a Python script to demultiplex libraries and trim off primer sequences. With +a standard alignment software the required bam files can be then be +generated.") + (license license:gpl3+))) |