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gnu: r-msnid: Move to (gnu packages bioconductor).

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* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
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zimoun 2021-05-21 22:25:38 +02:00 committed by Ricardo Wurmus
parent 537d48d869
commit 8c7c78bfce
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2 changed files with 52 additions and 52 deletions
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52
gnu/packages/bioconductor.scm
View file

@ -2517,6 +2517,58 @@ (define-public r-limma
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
(define-public r-msnid
(package
(name "r-msnid")
(version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
"05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-annotationhub" ,r-annotationhub)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biocstyle" ,r-biocstyle)
("r-biostrings" ,r-biostrings)
("r-data-table" ,r-data-table)
("r-doparallel" ,r-doparallel)
("r-dplyr" ,r-dplyr)
("r-foreach" ,r-foreach)
("r-ggplot2" ,r-ggplot2)
("r-iterators" ,r-iterators)
("r-msnbase" ,r-msnbase)
("r-msmstests" ,r-msmstests)
("r-mzid" ,r-mzid)
("r-mzr" ,r-mzr)
("r-protgenerics" ,r-protgenerics)
("r-purrr" ,r-purrr)
("r-r-cache" ,r-r-cache)
("r-rcpp" ,r-rcpp)
("r-reshape2" ,r-reshape2)
("r-rlang" ,r-rlang)
("r-runit" ,r-runit)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-xtable" ,r-xtable)))
(home-page "https://bioconductor.org/packages/MSnID")
(synopsis "Utilities for LC-MSn proteomics identifications")
(description
"This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
from mzIdentML (leveraging the mzID package) or text files. After collating
the search results from multiple datasets it assesses their identification
quality and optimize filtering criteria to achieve the maximum number of
identifications while not exceeding a specified false discovery rate. It also
contains a number of utilities to explore the MS/MS results and assess missed
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
(define-public r-rbgl
(package
(name "r-rbgl")

52
gnu/packages/bioinformatics.scm
View file

@ -9449,58 +9449,6 @@ (define-public r-msnbase
of mass spectrometry based proteomics data.")
(license license:artistic2.0)))
(define-public r-msnid
(package
(name "r-msnid")
(version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
"05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-annotationhub" ,r-annotationhub)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biocstyle" ,r-biocstyle)
("r-biostrings" ,r-biostrings)
("r-data-table" ,r-data-table)
("r-doparallel" ,r-doparallel)
("r-dplyr" ,r-dplyr)
("r-foreach" ,r-foreach)
("r-ggplot2" ,r-ggplot2)
("r-iterators" ,r-iterators)
("r-msnbase" ,r-msnbase)
("r-msmstests" ,r-msmstests)
("r-mzid" ,r-mzid)
("r-mzr" ,r-mzr)
("r-protgenerics" ,r-protgenerics)
("r-purrr" ,r-purrr)
("r-r-cache" ,r-r-cache)
("r-rcpp" ,r-rcpp)
("r-reshape2" ,r-reshape2)
("r-rlang" ,r-rlang)
("r-runit" ,r-runit)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-xtable" ,r-xtable)))
(home-page "https://bioconductor.org/packages/MSnID")
(synopsis "Utilities for LC-MSn proteomics identifications")
(description
"This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
from mzIdentML (leveraging the mzID package) or text files. After collating
the search results from multiple datasets it assesses their identification
quality and optimize filtering criteria to achieve the maximum number of
identifications while not exceeding a specified false discovery rate. It also
contains a number of utilities to explore the MS/MS results and assess missed
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
(define-public r-aroma-light
(package
(name "r-aroma-light")