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spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.66 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=gjxnfeuW; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: D878A1A252 X-Spam-Score: 2.66 X-Migadu-Scanner: scn0.migadu.com X-TUID: QrHLIQAiJ3H8 * gnu/packages/bioinformatics.scm (r-msnid): Move from here... * gnu/packages/bioconductor.scm (r-msnid): ...to here. --- gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 52 --------------------------------- 2 files changed, 52 insertions(+), 52 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 923413135b..b5787cb207 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -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") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c9288c6b0..5c2abe6e94 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") -- 2.30.1