GNU bug report logs - #56024
[PATCH] gnu: Add r-alpine.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#56024: closed ([PATCH] gnu: Add r-alpine.)
Date: Thu, 24 Nov 2022 13:45:03 +0000

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Your message dated Thu, 24 Nov 2022 14:44:26 +0100
with message-id <8735a8piux.fsf <at> elephly.net>
and subject line [PATCH] gnu: Add r-alpine.
has caused the debbugs.gnu.org bug report #56024,
regarding [PATCH] gnu: Add r-alpine.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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56024: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56024
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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-alpine.
Date: Thu, 16 Jun 2022 19:00:48 +0200

* gnu/packages/bioconductor.scm (r-alpine): New variable.
---
 gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

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
   (package
     (name "r-aneufinder")

base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb
-- 
2.36.1

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 56024-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-alpine.
Date: Thu, 24 Nov 2022 14:44:26 +0100

Applied, thanks!

-- 
Ricardo

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