@@ -2312,6 +2312,58 @@ and the assessment of differential expression. The analysis methods apply to
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")
@@ -9275,58 +9275,6 @@ structure (pcaRes) to provide a common interface to the PCA results.")
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")