{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:32:31Z","timestamp":1778635951089,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: High-throughput sequencing of transcriptomes (RNA-Seq) has become a powerful tool to study gene expression. Here we present an R package, rSeqNP, which implements a non-parametric approach to test for differential expression and splicing from RNA-Seq data. rSeqNP uses permutation tests to access statistical significance and can be applied to a variety of experimental designs. By combining information across isoforms, rSeqNP is able to detect more differentially expressed or spliced genes from RNA-Seq data.<\/jats:p>\n               <jats:p>Availability and implementation: The R package with its source code and documentation are freely available at http:\/\/www-personal.umich.edu\/\u223cjianghui\/rseqnp\/.<\/jats:p>\n               <jats:p>Contact: \u00a0jianghui@umich.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv119","type":"journal-article","created":{"date-parts":[[2015,2,26]],"date-time":"2015-02-26T15:34:19Z","timestamp":1424964859000},"page":"2222-2224","source":"Crossref","is-referenced-by-count":13,"title":["rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data"],"prefix":"10.1093","volume":"31","author":[{"given":"Yang","family":"Shi","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arul M.","family":"Chinnaiyan","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"1 Department of Biostatistics, 2Michigan Center for Translational Pathology, 3Department of Pathology, 4Comprehensive Cancer Center, 5Howard Hughes Medical Institute and 6Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,2,24]]},"reference":[{"key":"2023020202133776300_btv119-B1","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1093\/bioinformatics\/bts260","article-title":"Identifying differentially expressed transcripts from RNA-seq data with biological variation","volume":"28","author":"Glaus","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020202133776300_btv119-B2","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btp113","article-title":"Statistical inferences for isoform expression in RNA-Seq","volume":"25","author":"Jiang","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202133776300_btv119-B3","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1093\/bioinformatics\/btt087","article-title":"EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq 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Bioinf"},{"key":"2023020202133776300_btv119-B10","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"Trapnell","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2023020202133776300_btv119-B11","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1007\/s12561-011-9052-3","article-title":"A hierarchical bayesian model for estimating and inferring differential isoform expression for multi-sample RNA-Seq data","volume":"5","author":"Vardhanabhuti","year":"2013","journal-title":"Stat. Biosci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/13\/2222\/49034520\/bioinformatics_31_13_2222.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/13\/2222\/49034520\/bioinformatics_31_13_2222.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:39:57Z","timestamp":1675309197000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/13\/2222\/196264"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,2,24]]},"references-count":11,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2015,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv119","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,7,1]]},"published":{"date-parts":[[2015,2,24]]}}}