GNU bug report logs - #58522
[PATCH] gnu: Add r-fishpond. X-Debbugs-Cc: rekado@elephly.net

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: bug#58522: closed ([PATCH] gnu: Add r-fishpond.)
Date: Thu, 27 Oct 2022 13:26:02 +0000

[Message part 1 (text/plain, inline)]

Your bug report

#58522: [PATCH] gnu: Add r-fishpond. X-Debbugs-Cc: rekado <at> elephly.net

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 58522 <at> debbugs.gnu.org.

-- 
58522: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=58522
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 58522-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add r-fishpond.
Date: Thu, 27 Oct 2022 15:24:58 +0200

Applied with minor changes to the description.
Thanks!

-- 
Ricardo

[Message part 3 (message/rfc822, inline)]

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-fishpond. X-Debbugs-Cc: rekado <at> elephly.net
Date: Fri, 14 Oct 2022 19:01:42 +0200

* gnu/packages/bioconductor.scm (r-fishpond): New variable.
---
 gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ecb60f2e24..c23520175d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14522,6 +14522,44 @@ (define-public r-rgraphviz
 objects from the @code{graph} package.")
     (license license:epl1.0)))
 
+(define-public r-fishpond
+  (package
+    (name "r-fishpond")
+    (version "2.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "fishpond" version))
+              (sha256
+               (base32
+                "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym"))))
+    (properties `((upstream-name . "fishpond")))
+    (build-system r-build-system)
+    (inputs (list zlib))
+    (propagated-inputs
+      (list r-abind
+            r-genomicranges
+            r-gtools
+            r-iranges
+            r-jsonlite
+            r-matrix
+            r-matrixstats
+            r-qvalue
+            r-rcpp
+            r-s4vectors
+            r-singlecellexperiment
+            r-summarizedexperiment
+            r-svmisc))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/mikelove/fishpond")
+    (synopsis "Downstream methods and tools for expression data")
+    (description
+     "The @code{fishpond} package contains methods for differential transcript
+and gene expression analysis of RNA-seq data using inferential replicates for
+uncertainty of abundance quantification, as generated by Gibbs sampling or
+bootstrap sampling.  Also the package contains a number of utilities for working
+with @code{Salmon} and @code{Alevin} quantification files.")
+    (license license:gpl2)))
+
 (define-public r-fithic
   (package
     (name "r-fithic")

base-commit: 10d429f2fce321d8285684503094694ec3979865
-- 
2.37.3

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