MadalinIonel.Patrascu@mdc-berlin.de wrote 3 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
31f4f886465f473f9936beeaba8892ff@mdc-berlin.de
Add r-xina and it's dependencies: r-stringdb and r-alluvial
- Done
Details
- 3 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 1/3] gnu: Add r-alluvial.
(address . 51513@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20211030155506.28269-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-alluvial): New variable.
---
gnu/packages/cran.scm | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
Toggle diff (33 lines)
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
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 2/3] gnu: Add r-stringdb.
(address . 51513@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20211030155506.28269-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-stringdb): New variable.
---
gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
Toggle diff (46 lines)
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
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 3/3] gnu: Add r-xina.
(address . 51513@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20211030155506.28269-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-xina): New variable.
---
gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
Toggle diff (49 lines)
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
Ricardo Wurmus wrote 3 years ago
Re: [PATCH 1/3] gnu: Add r-alluvial.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 51513-done@debbugs.gnu.org)
87ee72os51.fsf@elephly.net
Thanks for the patches! I applied them all with minor changes to
indentation and description.
--
Ricardo
Closed
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