From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 16/16] gnu: Add r-msnid. Date: Tue, 17 Jan 2017 15:11:41 +0100 Message-ID: <20170117141141.11694-17-rekado@elephly.net> References: <20170117141141.11694-1-rekado@elephly.net> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40563) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTUVR-0007lr-B2 for guix-devel@gnu.org; Tue, 17 Jan 2017 09:13:02 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTUVN-00078r-ED for guix-devel@gnu.org; Tue, 17 Jan 2017 09:13:01 -0500 Received: from sender163-mail.zoho.com ([74.201.84.163]:21033) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cTUVN-00077x-5s for guix-devel@gnu.org; Tue, 17 Jan 2017 09:12:57 -0500 In-Reply-To: <20170117141141.11694-1-rekado@elephly.net> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (r-msnid): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index abe5c9294..c60bedce4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8463,3 +8463,42 @@ structure (pcaRes) to provide a common interface to the PCA results.") "This package provides basic plotting, data manipulation and processing of MS-based proteomics data.") (license license:artistic2.0))) + +(define-public r-msnid + (package + (name "r-msnid") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnID" version)) + (sha256 + (base32 + "0fkk3za39cxi0jyxmagmycjdslr2xf6vg3ylz14jyffqi0blw9d5")))) + (properties `((upstream-name . "MSnID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-data-table" ,r-data-table) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-msnbase" ,r-msnbase) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-protgenerics" ,r-protgenerics) + ("r-r-cache" ,r-r-cache) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2))) + (home-page "http://bioconductor.org/packages/MSnID") + (synopsis "Utilities for LC-MSn proteomics identifications") + (description + "This package extracts 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))) -- 2.11.0