{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T09:45:12Z","timestamp":1781516712572,"version":"3.54.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T00:00:00Z","timestamp":1499731200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["SFB1243"],"award-info":[{"award-number":["SFB1243"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The R package and associated tutorial are freely available at https:\/\/github.com\/bvieth\/powsimR.<\/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\/btx435","type":"journal-article","created":{"date-parts":[[2017,7,4]],"date-time":"2017-07-04T07:09:43Z","timestamp":1499152183000},"page":"3486-3488","source":"Crossref","is-referenced-by-count":155,"title":["powsimR: power analysis for bulk and single cell RNA-seq experiments"],"prefix":"10.1093","volume":"33","author":[{"given":"Beate","family":"Vieth","sequence":"first","affiliation":[{"name":"Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Ziegenhain","sequence":"additional","affiliation":[{"name":"Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Swati","family":"Parekh","sequence":"additional","affiliation":[{"name":"Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfgang","family":"Enard","sequence":"additional","affiliation":[{"name":"Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ines","family":"Hellmann","sequence":"additional","affiliation":[{"name":"Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,7,11]]},"reference":[{"key":"2023051506354725800_btx435-B1","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1534\/genetics.110.114983","article-title":"Statistical design and analysis of RNA sequencing data","volume":"185","author":"Auer","year":"2010","journal-title":"Genetics"},{"key":"2023051506354725800_btx435-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":"2023051506354725800_btx435-B3","doi-asserted-by":"crossref","first-page":"13.","DOI":"10.1186\/s13059-016-0881-8","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol"},{"key":"2023051506354725800_btx435-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-015-0844-5","article-title":"MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data","volume":"16","author":"Finak","year":"2015","journal-title":"Genome Biol"},{"key":"2023051506354725800_btx435-B5","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nmeth.2930","article-title":"Validation of noise models for single-cell transcriptomics","volume":"11","author":"Gr\u00fcn","year":"2014","journal-title":"Nat. Methods"},{"key":"2023051506354725800_btx435-B6","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1093\/bioinformatics\/btv569","article-title":"Generalized empirical bayesian methods for discovery of differential data in high-throughput biology","volume":"32","author":"Hardcastle","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051506354725800_btx435-B7","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.celrep.2012.08.003","article-title":"CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification","volume":"2","author":"Hashimshony","year":"2012","journal-title":"Cell Rep"},{"key":"2023051506354725800_btx435-B8","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1038\/nmeth.2967","article-title":"Bayesian approach to single-cell differential expression analysis","volume":"11","author":"Kharchenko","year":"2014","journal-title":"Nat. Methods"},{"key":"2023051506354725800_btx435-B9","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2015.04.044","article-title":"Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells","volume":"161","author":"Klein","year":"2015","journal-title":"Cell"},{"key":"2023051506354725800_btx435-B10","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.stem.2015.09.011","article-title":"Single cell RNA-Sequencing of pluripotent states unlocks modular transcriptional variation","volume":"17","author":"Kolodziejczyk","year":"2015","journal-title":"Cell Stem Cell"},{"key":"2023051506354725800_btx435-B11","doi-asserted-by":"crossref","first-page":"222.","DOI":"10.1186\/s13059-016-1077-y","article-title":"A statistical approach for identifying differential distributions in single-cell RNA-seq experiments","volume":"17","author":"Korthauer","year":"2016","journal-title":"Genome Biol"},{"key":"2023051506354725800_btx435-B12","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 experiments","volume":"29","author":"Leng","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051506354725800_btx435-B13","doi-asserted-by":"crossref","first-page":"550.","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023051506354725800_btx435-B14","doi-asserted-by":"crossref","first-page":"75.","DOI":"10.1186\/s13059-016-0947-7","article-title":"Pooling across cells to normalize single-cell RNA sequencing data with many zero counts","volume":"17","author":"Lun","year":"2016","journal-title":"Genome Biol"},{"key":"2023051506354725800_btx435-B15","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"2023051506354725800_btx435-B16","doi-asserted-by":"crossref","first-page":"e0119254.","DOI":"10.1371\/journal.pone.0119254","article-title":"Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data","volume":"10","author":"Mi","year":"2015","journal-title":"PLoS One"},{"key":"2023051506354725800_btx435-B17","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"2023051506354725800_btx435-B18","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nprot.2014.006","article-title":"Full-length RNA-seq from single cells using smart-seq2","volume":"9","author":"Picelli","year":"2014","journal-title":"Nat. Protoc"},{"key":"2023051506354725800_btx435-B19","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbw144","article-title":"Feasibility of sample size calculation for RNA-seq studies","author":"Poplawski","year":"2017","journal-title":"Brief. Bioinform"},{"key":"2023051506354725800_btx435-B20","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nmeth.4150","article-title":"Single-cell mRNA quantification and differential analysis with census","volume":"14","author":"Qiu","year":"2017","journal-title":"Nat. Methods"},{"key":"2023051506354725800_btx435-B21","doi-asserted-by":"crossref","first-page":"e47.","DOI":"10.1093\/nar\/gkv007","article-title":"Limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023051506354725800_btx435-B22","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":"2023051506354725800_btx435-B23","author":"Schurch","year":"2016"},{"key":"2023051506354725800_btx435-B24","first-page":"gkv806.","article-title":"ROTS: reproducible RNA-seq biomarker detector\u2014prognostic markers for clear cell renal cell cancer","author":"Seyednasrollah","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023051506354725800_btx435-B25","author":"Soumillon","year":"2014"},{"key":"2023051506354725800_btx435-B26","first-page":"e140.","article-title":"Data quality aware analysis of differential expression in RNA-seq with NOISeq R\/Bioc package","volume":"43","author":"Tarazona","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023051506354725800_btx435-B27","doi-asserted-by":"crossref","first-page":"2128","DOI":"10.1093\/bioinformatics\/btw202","article-title":"Beta-Poisson model for single-cell RNA-seq data analyses","volume":"32","author":"Vu","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051506354725800_btx435-B28","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/nmeth.2694","article-title":"Quantitative assessment of single-cell RNA-sequencing methods","volume":"11","author":"Wu","year":"2014","journal-title":"Nat. Methods"},{"key":"2023051506354725800_btx435-B29","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1093\/biostatistics\/kxs033","article-title":"A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data","volume":"14","author":"Wu","year":"2013","journal-title":"Biostatistics"},{"key":"2023051506354725800_btx435-B30","doi-asserted-by":"crossref","first-page":"14049.","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun"},{"key":"2023051506354725800_btx435-B31","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1016\/j.molcel.2017.01.023","article-title":"Comparative analysis of Single-Cell RNA sequencing methods","volume":"65","author":"Ziegenhain","year":"2017","journal-title":"Mol. Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/21\/3486\/50315494\/bioinformatics_33_21_3486.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/21\/3486\/50315494\/bioinformatics_33_21_3486.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T02:36:12Z","timestamp":1684118172000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/21\/3486\/3952669"}},"subtitle":[],"editor":[{"given":"Ivo","family":"Hofacker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,7,11]]},"references-count":31,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2017,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx435","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/117150","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,11,1]]},"published":{"date-parts":[[2017,7,11]]}}}