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author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2022-06-16 19:00:48 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-11-23 13:57:43 +0100 |
commit | 093bf20cdc54add190b1184f548cb5d3a97c6ad1 (patch) | |
tree | 44f26b3f50b41e298d4ea1fbdab22ddba6686328 /gnu/packages | |
parent | 7fa8c0575303908f921a2032eeeaa9c34e37fbdb (diff) | |
download | guix-093bf20cdc54add190b1184f548cb5d3a97c6ad1.tar.gz guix-093bf20cdc54add190b1184f548cb5d3a97c6ad1.zip |
gnu: Add r-alpine.
* gnu/packages/bioconductor.scm (r-alpine): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r-- | gnu/packages/bioconductor.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f3b67fd2bf..45a511cf13 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2276,6 +2276,47 @@ paired or unpaired study designs.") ;; package's LICENSE is specified as GPL-3. (license (list license:agpl3+ license:gpl2+ license:gpl3)))) +(define-public r-alpine + (package + (name "r-alpine") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alpine" version)) + (sha256 + (base32 + "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9")))) + (properties `((upstream-name . "alpine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alpine") + (synopsis "Modeling and correcting fragment sequence bias") + (description + "The package @code{alpine} helps to model bias parameters and then using +those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a +package for estimating and visualizing many forms of sample-specific biases that +can arise in RNA-seq, including fragment length distribution, positional bias on +the transcript, read start bias (random hexamer priming), and fragment GC-content +(amplification). It also offers bias-corrected estimates of transcript +abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million +mapped reads). It is currently designed for un-stranded paired-end RNA-seq +data.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") |