{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T04:48:55Z","timestamp":1785905335471,"version":"3.56.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T00:00:00Z","timestamp":1581897600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"UGent Special Research Fund Concerted Research Actions","award":["BOF16-GOA-023"],"award-info":[{"award-number":["BOF16-GOA-023"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>SPsimSeq is a semi-parametric simulation method to generate bulk and single-cell RNA-sequencing data. It is designed to simulate gene expression data with maximal retention of the characteristics of real data. It is reasonably flexible to accommodate a wide range of experimental scenarios, including different sample sizes, biological signals (differential expression) and confounding batch effects.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The R package and associated documentation is available from https:\/\/github.com\/CenterForStatistics-UGent\/SPsimSeq.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa105","type":"journal-article","created":{"date-parts":[[2020,2,11]],"date-time":"2020-02-11T07:10:16Z","timestamp":1581405016000},"page":"3276-3278","source":"Crossref","is-referenced-by-count":48,"title":["SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7773-0621","authenticated-orcid":false,"given":"Alemu Takele","family":"Assefa","sequence":"first","affiliation":[{"name":"Data Analysis and Mathematical Modeling"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo","family":"Vandesompele","sequence":"additional","affiliation":[{"name":"Biomolecular Medicine"},{"name":"Cancer Research Institute Ghent"},{"name":"Center for Medical Genetics , Ghent University, Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Thas","sequence":"additional","affiliation":[{"name":"Data Analysis and Mathematical Modeling"},{"name":"Cancer Research Institute Ghent"},{"name":"National Institute for Applied Statistics Research Australia (NIASRA) , University of Wollongong, Wollongong, Australia"},{"name":"Data Science Institute , I-BioStat, Hasselt University, Hasselt, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,2,17]]},"reference":[{"key":"2023013112025799900_btaa105-B1","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1186\/s13059-018-1466-5","article-title":"Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data","volume":"19","author":"Assefa","year":"2018","journal-title":"Genome Biol"},{"key":"2023013112025799900_btaa105-B2","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/s13059-016-0927-y","article-title":"Design and computational analysis of single-cell RNA-sequencing experiments","volume":"17","author":"Bacher","year":"2016","journal-title":"Genome Biol"},{"key":"2023013112025799900_btaa105-B3","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1093\/bioinformatics\/btv124","article-title":"SimSeq: a nonparametric approach to simulation of RNA-sequence datasets","volume":"31","author":"Benidt","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013112025799900_btaa105-B4","author":"Cario","year":"1997"},{"key":"2023013112025799900_btaa105-B5","doi-asserted-by":"crossref","first-page":"2431","DOI":"10.1214\/aos\/1032181161","article-title":"Using specially designed exponential families for density estimation","volume":"24","author":"Efron","year":"1996","journal-title":"Ann. 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