{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T22:29:32Z","timestamp":1778884172042,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1525,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA sequencing is becoming a standard for expression profiling experiments and many tools have been developed in the past few years to analyze RNA-Seq data. Numerous \u2018Bioconductor\u2019 packages are available for next-generation sequencing data loading in R, e.g. ShortRead and Rsamtools as well as to perform differential gene expression analyses, e.g. DESeq and edgeR. However, the processing tasks lying in between these require the precise interplay of many Bioconductor packages, e.g. Biostrings, IRanges or external solutions are to be sought.<\/jats:p>\n               <jats:p>Results: We developed \u2018easyRNASeq\u2019, an R package that simplifies the processing of RNA sequencing data, hiding the complex interplay of the required packages behind a single functionality.<\/jats:p>\n               <jats:p>Availability: The package is implemented in R (as of version 2.15) and is available from Bioconductor (as of version 2.10) at the URL: http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/easyRNASeq.html, where installation and usage instructions can be found.<\/jats:p>\n               <jats:p>Contact: \u00a0delhomme@embl.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts477","type":"journal-article","created":{"date-parts":[[2012,7,31]],"date-time":"2012-07-31T06:55:55Z","timestamp":1343717755000},"page":"2532-2533","source":"Crossref","is-referenced-by-count":91,"title":["easyRNASeq: a bioconductor package for processing RNA-Seq data"],"prefix":"10.1093","volume":"28","author":[{"given":"Nicolas","family":"Delhomme","sequence":"first","affiliation":[{"name":"1 Genome Biology Computational Support and 2Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isma\u00ebl","family":"Padioleau","sequence":"additional","affiliation":[{"name":"1 Genome Biology Computational Support and 2Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eileen E.","family":"Furlong","sequence":"additional","affiliation":[{"name":"1 Genome Biology Computational Support and 2Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"},{"name":"1 Genome Biology Computational Support and 2Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lars M.","family":"Steinmetz","sequence":"additional","affiliation":[{"name":"1 Genome Biology Computational Support and 2Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"},{"name":"1 Genome Biology Computational Support and 2Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,7,30]]},"reference":[{"issue":"10","key":"2023012513141719300_bts477-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":"2023012513141719300_bts477-B2","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"Biomart and bioconductor: a powerful link between biological databases and microarray data analysis","volume":"21","author":"Durinck","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012513141719300_bts477-B3","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023012513141719300_bts477-B4","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1002\/j.1538-7305.1950.tb00463.x","article-title":"Error detecting and error correcting codes","volume":"29","author":"Hamming","year":"1950","journal-title":"Bell Syst. 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