GNU bug report logs - #54991
gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.

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 54991 in the body.
You can then email your comments to 54991 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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: gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.
Date: Sun, 17 Apr 2022 13:41:08 +0000

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

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

Message #8 received at 54991 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <54991 <at> debbugs.gnu.org>
Subject: [PATCH 3/3] gnu: Add r-adductomicsr.
Date: Sun, 17 Apr 2022 17:10:46 +0200

* gnu/packages/bioconductor.scm (r-adductomicsr): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6e4ed31154..2cd4c89aa9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1605,6 +1605,50 @@ (define-public r-absseq
 ranking by fold-change and visualization.")
     (license license:gpl3+)))
 
+(define-public r-adductomicsr
+  (package
+    (name "r-adductomicsr")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "adductomicsR" version))
+              (sha256
+               (base32
+                "0cnvxrk0h3r6jpa4g4qismg6zk5c7rf8lqixg89c24i98gffkbcl"))))
+    (properties `((upstream-name . "adductomicsR")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-adductdata
+                             r-ade4
+                             r-annotationhub
+                             r-bootstrap
+                             r-data-table
+                             r-dosnow
+                             r-dplyr
+                             r-dt
+                             r-experimenthub
+                             r-fastcluster
+                             r-foreach
+                             r-fpc
+                             r-mzr
+                             r-orgmassspecr
+                             r-pastecs
+                             r-pracma
+                             r-rcppeigen
+                             r-reshape2
+                             r-rvest
+                             r-smoother
+                             r-zoo))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/adductomicsR")
+    (synopsis "Processing of adductomic mass spectral datasets")
+    (description
+     "This package @code{adductomicsR} processes data generated by the
+@dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
+peptides from spectra that has been corrected for mass drift and retention time
+drift and quantifies level mass spectral peaks from @dfn{first stage of mass
+spectrometry} (MS1) data.")
+    (license license:artistic2.0)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")
-- 
2.34.0

Message #11 received at 54991 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <54991 <at> debbugs.gnu.org>
Subject: [PATCH 1/3] gnu: Add r-adductdata.
Date: Sun, 17 Apr 2022 17:10:44 +0200

* gnu/packages/bioconductor.scm (r-adductdata): New variable.
---
 gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bec3496057..6e4ed31154 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1166,6 +1166,30 @@ (define-public r-abadata
 All datasets are restricted to protein coding genes.")
     (license license:gpl2+)))
 
+(define-public r-adductdata
+  (package
+    (name "r-adductdata")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "adductData" version
+                                     'experiment))
+              (sha256
+               (base32
+                "0bp74p06gskwn2xl1srpnmsq27ajsrlynkzw6fcmvwwjcrzljmnj"))))
+    (properties `((upstream-name . "adductData")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationhub r-experimenthub))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/adductData")
+    (synopsis
+     "Data from untargeted mass spectrometry of modifications to Cys34")
+    (description
+     "This package contains data from untargeted @dfn{mass spectrometry} (MS)
+of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
+albumin} (HSA).")
+    (license license:artistic2.0)))
+
 (define-public r-aneufinderdata
   (package
    (name "r-aneufinderdata")

base-commit: 0c89fe9e17dc9e628c73959289464ac5f146c7cd
-- 
2.34.0

Message #14 received at 54991 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <54991 <at> debbugs.gnu.org>
Subject: [PATCH 2/3] gnu: Add r-orgmassspecr.
Date: Sun, 17 Apr 2022 17:10:45 +0200

* gnu/packages/cran.scm (r-orgmassspecr): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bc95eee065..17396d130c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1068,6 +1068,28 @@ (define-public r-oenb
 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
     (license license:gpl2+)))
 
+(define-public r-orgmassspecr
+  (package
+    (name "r-orgmassspecr")
+    (version "0.5-3")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "OrgMassSpecR" version))
+              (sha256
+               (base32
+                "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
+    (properties `((upstream-name . "OrgMassSpecR")))
+    (build-system r-build-system)
+    (native-inputs (list r-knitr))
+    (home-page "http://OrgMassSpec.github.io/")
+    (synopsis "Organic or biological mass spectrometry data analysis")
+    (description
+     "This package @code{OrgMassSpecR} is an extension of the @code{R}
+statistical computing language.  It contains functions to assist with organic
+or biological mass spectrometry data analysis.  Mass spectral libraries are
+available as companion packages.")
+    (license license:bsd-2)))
+
 (define-public r-scales
   (package
     (name "r-scales")
-- 
2.34.0

Message #19 received at 54991-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 54991-done <at> debbugs.gnu.org
Subject: gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.
Date: Mon, 02 May 2022 15:21:16 +0200

Applied, thanks!

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.