{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T20:18:12Z","timestamp":1773173892317,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"<jats:p>Summary: \u00a0compcodeR is an R package for benchmarking of differential expression analysis methods, in particular, methods developed for analyzing RNA-seq data. The package provides functionality for simulating realistic RNA-seq count datasets, an interface to several of the most commonly used differential expression analysis methods and extensive functionality for evaluating and comparing different approaches on real and simulated data.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0compcodeR is available from http:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/compcodeR.html<\/jats:p>\n               <jats:p>Contact: \u00a0Charlotte.Soneson@isb-sib.ch or charlottesoneson@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu324","type":"journal-article","created":{"date-parts":[[2014,5,10]],"date-time":"2014-05-10T00:17:52Z","timestamp":1399681072000},"page":"2517-2518","source":"Crossref","is-referenced-by-count":55,"title":["compcodeR\u2014an R package for benchmarking differential expression methods for RNA-seq data"],"prefix":"10.1093","volume":"30","author":[{"given":"Charlotte","family":"Soneson","sequence":"first","affiliation":[{"name":"1Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Quartier Sorge, CH-1015 Lausanne, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2014,5,9]]},"reference":[{"key":"2023012711525790300_btu324-B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023012711525790300_btu324-B2","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1186\/1471-2105-11-422","article-title":"baySeq: empirical Bayesian methods for identifying differential expression in sequence count data","volume":"11","author":"Hardcastle","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012711525790300_btu324-B3","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012711525790300_btu324-B4","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1186\/1471-2164-13-484","article-title":"Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing","volume":"13","author":"Robles","year":"2012","journal-title":"BMC Genomics"},{"key":"2023012711525790300_btu324-B5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-2105-14-91","article-title":"A comparison of methods for differential expression analysis of RNA-seq data","volume":"14","author":"Soneson","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023012711525790300_btu324-B6","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1101\/gr.124321.111","article-title":"Differential expression in RNA-seq: a matter of depth","volume":"21","author":"Tarazona","year":"2011","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2517\/48927344\/bioinformatics_30_17_2517.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2517\/48927344\/bioinformatics_30_17_2517.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:11:09Z","timestamp":1674821469000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/17\/2517\/2748207"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,9]]},"references-count":6,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2014,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu324","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,9]]}}}