GNU bug report logs -
#51513
Add r-xina and it's dependencies: r-stringdb and r-alluvial
Previous Next
To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 51513 in the body.
You can then email your comments to 51513 AT debbugs.gnu.org in the normal way.
Toggle the display of automated, internal messages from the tracker.
Report forwarded
to
guix-patches <at> gnu.org
:
bug#51513
; Package
guix-patches
.
(Sat, 30 Oct 2021 15:53:02 GMT)
Full text and
rfc822 format available.
Acknowledgement sent
to
"MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>
:
New bug report received and forwarded. Copy sent to
guix-patches <at> gnu.org
.
(Sat, 30 Oct 2021 15:53:02 GMT)
Full text and
rfc822 format available.
Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
[Message part 2 (text/html, inline)]
Information forwarded
to
guix-patches <at> gnu.org
:
bug#51513
; Package
guix-patches
.
(Sat, 30 Oct 2021 15:56:01 GMT)
Full text and
rfc822 format available.
Message #8 received at 51513 <at> debbugs.gnu.org (full text, mbox):
* 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
Information forwarded
to
guix-patches <at> gnu.org
:
bug#51513
; Package
guix-patches
.
(Sat, 30 Oct 2021 15:56:02 GMT)
Full text and
rfc822 format available.
Message #11 received at 51513 <at> debbugs.gnu.org (full text, mbox):
* 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
Information forwarded
to
guix-patches <at> gnu.org
:
bug#51513
; Package
guix-patches
.
(Sat, 30 Oct 2021 15:56:02 GMT)
Full text and
rfc822 format available.
Message #14 received at 51513 <at> debbugs.gnu.org (full text, mbox):
* 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
Reply sent
to
Ricardo Wurmus <rekado <at> elephly.net>
:
You have taken responsibility.
(Sat, 27 Nov 2021 09:39:02 GMT)
Full text and
rfc822 format available.
Notification sent
to
"MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>
:
bug acknowledged by developer.
(Sat, 27 Nov 2021 09:39:02 GMT)
Full text and
rfc822 format available.
Message #19 received at 51513-done <at> debbugs.gnu.org (full text, mbox):
Thanks for the patches! I applied them all with minor changes to
indentation and description.
--
Ricardo
bug archived.
Request was from
Debbugs Internal Request <help-debbugs <at> gnu.org>
to
internal_control <at> debbugs.gnu.org
.
(Sat, 25 Dec 2021 12:24:05 GMT)
Full text and
rfc822 format available.
This bug report was last modified 2 years and 84 days ago.
Previous Next
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.