Subject: bug#56024: closed ([PATCH] gnu: Add r-alpine.)

From: [email-masked] (GNU bug Tracking System)
Date: Thu, 24 Nov 2022 13:45:03 +0000

Your bug report

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

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
56024: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56024
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: [PATCH] gnu: Add r-alpine.
From: Ricardo Wurmus <[email-masked]>
To: [email-masked]
Date: Thu, 24 Nov 2022 14:44:26 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

Applied, thanks!

-- 
Ricardo

Subject: [PATCH] gnu: Add r-alpine.
From: Mădălin Ionel Patrașcu<[email-masked]>
To: <[email-masked]>
Date: Thu, 16 Jun 2022 19:00:48 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

* 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