GNU bug report logs - #51513
Add r-xina and it's dependencies: r-stringdb and r-alluvial

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: Add r-xina and it's dependencies: r-stringdb and r-alluvial
Date: Sat, 30 Oct 2021 15:52:04 +0000

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[Message part 2 (text/html, inline)]

Message #8 received at 51513 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <51513 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 1/3] gnu: Add r-alluvial.
Date: Sat, 30 Oct 2021 17:55:04 +0200

* gnu/packages/cran.scm (r-alluvial): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 792ea2a75b..0e79ea0ef2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7070,6 +7070,26 @@ (define-public r-algdesign
 and within plot factors interact.")
     (license license:gpl2+)))
 
+(define-public r-alluvial
+(package
+  (name "r-alluvial")
+  (version "0.1-2")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (cran-uri "alluvial" version))
+      (sha256
+        (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
+  (properties `((upstream-name . "alluvial")))
+  (build-system r-build-system)
+  (native-inputs `(("r-knitr" ,r-knitr)))
+  (home-page "https://github.com/mbojan/alluvial")
+  (synopsis "Creating parallel sets plots (Alluvial Diagrams)")
+  (description
+    "The package @code{r-alluvial} creates alluvial diagrams (also known as
+parallel sets plots) for multivariate and time series-like data.")
+  (license license:expat)))
+
 (define-public r-signal
   (package
     (name "r-signal")
-- 
2.33.0

Message #11 received at 51513 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <51513 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 2/3] gnu: Add r-stringdb.
Date: Sat, 30 Oct 2021 17:55:05 +0200

* gnu/packages/bioconductor.scm (r-stringdb): New variable.
---
 gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 90a0e1f288..f82427f831 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4337,6 +4337,39 @@ (define-public r-slingshot
 graph construction.")
    (license license:artistic2.0)))
 
+(define-public r-stringdb
+  (package
+    (name "r-stringdb")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "STRINGdb" version))
+       (sha256
+        (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm"))))
+    (properties `((upstream-name . "STRINGdb")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gplots" ,r-gplots)
+       ("r-hash" ,r-hash)
+       ("r-igraph" ,r-igraph)
+       ("r-plotrix" ,r-plotrix)
+       ("r-plyr" ,r-plyr)
+       ("r-png" ,r-png)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcurl" ,r-rcurl)
+       ("r-sqldf" ,r-sqldf)))
+    (home-page "https://git.bioconductor.org/packages/STRINGdb")
+    (synopsis "Searching tool for the retrieval of interacting proteins database")
+    (description
+     "The @code{STRINGdb} package provides a R interface to the STRING
+protein-protein interactions database.  STRING (https://www.string-db.org) is a
+database of known and predicted protein-protein interactions.  The interactions
+include direct (physical) and indirect (functional) associations.  Each
+interaction is associated with a combined confidence score that integrates the
+various evidences.")
+    (license license:gpl2)))
+
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")
-- 
2.33.0

Message #14 received at 51513 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <51513 <at> debbugs.gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH 3/3] gnu: Add r-xina.
Date: Sat, 30 Oct 2021 17:55:06 +0200

* gnu/packages/bioconductor.scm (r-xina): New variable.
---
 gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f82427f831..a232c3fe61 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4660,6 +4660,42 @@ (define-public r-vsn
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
+(define-public r-xina
+  (package
+    (name "r-xina")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "XINA" version))
+       (sha256
+        (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp"))))
+    (properties `((upstream-name . "XINA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-alluvial" ,r-alluvial)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-igraph" ,r-igraph)
+       ("r-mclust" ,r-mclust)
+       ("r-plyr" ,r-plyr)
+       ("r-stringdb" ,r-stringdb)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://git.bioconductor.org/packages/XINA")
+    (synopsis "Identifying proteins that exhibit similar patterns")
+    (description
+     "The aim of @code{XINA} is to determine which proteins exhibit similar
+patterns within and across experimental conditions, since proteins with
+co-abundance patterns may have common molecular functions.  @code{XINA} imports
+multiple datasets, tags dataset in silico, and combines the data for subsequent
+subgrouping into multiple clusters.  The result is a single output depicting
+the variation across all conditions.  @code{XINA}, not only extracts
+coabundance profiles within and across experiments, but also incorporates
+protein-protein interaction databases and integrative resources such as
+@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
+molecular functions, respectively, and produces intuitive graphical outputs.")
+    (license license:gpl3)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
-- 
2.33.0

Message #19 received at 51513-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 51513-done <at> debbugs.gnu.org
Subject: Re: [PATCH 1/3] gnu: Add r-alluvial.
Date: Sat, 27 Nov 2021 10:35:34 +0100

Thanks for the patches!  I applied them all with minor changes to 
indentation and description.

-- 
Ricardo

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