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[bug#56024] gnu: Add r-alpine.

Message ID 20220616170048.28808-1-madalinionel.patrascu@mdc-berlin.de
State New
Headers show
Series [bug#56024] gnu: Add r-alpine. | expand


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Commit Message

Mădălin Ionel Patrașcu June 16, 2022, 5 p.m. UTC
* gnu/packages/bioconductor.scm (r-alpine): New variable.
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb
diff mbox series


diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..e0797206f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1987,6 +1987,46 @@  (define-public r-agimicrorna
 objects are used so that other packages could be used as well.")
     (license 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
     (name "r-aneufinder")