MadalinIonel.Patrascu@mdc-berlin.de wrote 3 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
d36bb448159f4c33950c0e82aad93758@mdc-berlin.de
gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.
- 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 3/3] gnu: Add r-adductomicsr.
(address . 54991@debbugs.gnu.org)
20220417151046.2206-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-adductomicsr): New variable.
---
gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
Toggle diff (57 lines)
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
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 1/3] gnu: Add r-adductdata.
(address . 54991@debbugs.gnu.org)
20220417151046.2206-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-adductdata): New variable.
---
gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
Toggle diff (39 lines)
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
Mădălin Ionel Patrașcu wrote 3 years ago
[PATCH 2/3] gnu: Add r-orgmassspecr.
(address . 54991@debbugs.gnu.org)
20220417151046.2206-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-orgmassspecr): New variable.
---
gnu/packages/cran.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
Toggle diff (35 lines)
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
Ricardo Wurmus wrote 3 years ago
gnu: Add r-adductomicsr, r-adductdata and r-orgmassspecr.
(address . 54991-done@debbugs.gnu.org)
87czgwxe79.fsf@elephly.net
Applied, thanks!
--
Ricardo
Closed
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