{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T05:45:39Z","timestamp":1782884739753,"version":"3.54.5"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":71,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http:\/\/www.bioconductor.org\/). A complete tutorial and a toy dataset are accompanying the packages.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw580","type":"journal-article","created":{"date-parts":[[2016,9,8]],"date-time":"2016-09-08T00:39:31Z","timestamp":1473295171000},"page":"135-136","source":"Crossref","is-referenced-by-count":341,"title":["DAPAR &amp; ProStaR: software to perform statistical analyses in quantitative discovery proteomics"],"prefix":"10.1093","volume":"33","author":[{"given":"Samuel","family":"Wieczorek","sequence":"first","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florence","family":"Combes","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cosmin","family":"Lazar","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quentin","family":"Giai Gianetto","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Gatto","sequence":"additional","affiliation":[{"name":"Computational Proteomics Unit, Cambridge, UK"},{"name":"Cambridge Center for Proteomics, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexia","family":"Dorffer","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Marie","family":"Hesse","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yohann","family":"Cout\u00e9","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myriam","family":"Ferro","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Bruley","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Burger","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Grenoble Alpes, BIG-BGE, Grenoble, France"},{"name":"CEA, BIG-BGE, Grenoble, France"},{"name":"INSERM, BGE, Grenoble, France"},{"name":"CNRS, BIG-BGE, Grenoble, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,9,6]]},"reference":[{"key":"2023020204203321300_btw580-B1","author":"Bolstad","year":"2007"},{"key":"2023020204203321300_btw580-B2","doi-asserted-by":"crossref","first-page":"2524","DOI":"10.1093\/bioinformatics\/btu305","article-title":"MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments","volume":"30","author":"Choi","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020204203321300_btw580-B3","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/bioinformatics\/btr645","article-title":"MSnbase-an R\/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation","volume":"28","author":"Gatto","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020204203321300_btw580-B4","author":"Hastie","year":"2001"},{"key":"2023020204203321300_btw580-B5","article-title":"imputeLCMD: a collection of methods for left-censored missing data imputation","author":"Lazar","year":"2015","journal-title":"CRAN"},{"key":"2023020204203321300_btw580-B6","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating and analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020204203321300_btw580-B7","doi-asserted-by":"crossref","first-page":"1556","DOI":"10.1093\/bioinformatics\/btn217","article-title":"Dante: a statistical tool for quantitative analysis of-omics data","volume":"24","author":"Polpitiya","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020204203321300_btw580-B8","first-page":"gkv007.","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020204203321300_btw580-B9","author":"Schafer","year":"2008"},{"key":"2023020204203321300_btw580-B10","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1093\/bioinformatics\/btm069","article-title":"pcaMethods\u2014a bioconductor package providing PCA methods for incomplete data","volume":"23","author":"Stacklies","year":"2007","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/1\/135\/49037276\/bioinformatics_33_1_135.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/1\/135\/49037276\/bioinformatics_33_1_135.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:21:02Z","timestamp":1675311662000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/1\/135\/2525689"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,9,6]]},"references-count":10,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw580","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,1,1]]},"published":{"date-parts":[[2016,9,6]]}}}