{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T12:04:52Z","timestamp":1770984292212,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,12,16]],"date-time":"2020-12-16T00:00:00Z","timestamp":1608076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2018YFC0910405"],"award-info":[{"award-number":["2018YFC0910405"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61922020"],"award-info":[{"award-number":["61922020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61771165"],"award-info":[{"award-number":["61771165"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91935302"],"award-info":[{"award-number":["91935302"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Processing raw reads of RNA-sequencing (RNA-seq) data, no matter public or newly sequenced data, involves a lot of specialized tools and technical configurations that are often unfamiliar and time-consuming to learn for non-bioinformatics researchers. Here, we develop the R package BP4RNAseq, which integrates the state-of-art tools from both alignment-based and alignment-free quantification workflows. The BP4RNAseq package is a highly automated tool using an optimized pipeline to improve the sensitivity and accuracy of RNA-seq analyses. It can take only two non-technical parameters and output six formatted gene expression quantification at gene and transcript levels. The package applies to both retrospective and newly generated bulk RNA-seq data analyses and is also applicable for single-cell RNA-seq analyses. It, therefore, greatly facilitates the application of RNA-seq.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The BP4RNAseq package for R and its documentation are freely available at https:\/\/github.com\/sunshanwen\/BP4RNAseq.<\/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\/btaa832","type":"journal-article","created":{"date-parts":[[2020,9,10]],"date-time":"2020-09-10T13:56:27Z","timestamp":1599746187000},"page":"1319-1321","source":"Crossref","is-referenced-by-count":64,"title":["BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4358-8636","authenticated-orcid":false,"given":"Shanwen","family":"Sun","sequence":"first","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China , Chengdu, 610054 China"}]},{"given":"Lei","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Electronic and Communication Engineering, Shenzhen Polytechnic , Shenzhen, 518055 China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China , Chengdu, 610054 China"},{"name":"State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University , Harbin, 150040, China"}]},{"given":"Guohua","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University , Harbin, 150040, China"},{"name":"Northeast Forestry University College of Information and Computer Engineering, , Harbin, 150040 China"}]}],"member":"286","published-online":{"date-parts":[[2020,12,16]]},"reference":[{"key":"2023051705211350600_btaa832-B1","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1093\/bioinformatics\/bts477","article-title":"easyRNASeq: a bioconductor package for processing RNA-Seq data","volume":"28","author":"Delhomme","year":"2012","journal-title":"Bioinformatics"},{"key":"2023051705211350600_btaa832-B2","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene expression omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2023051705211350600_btaa832-B3","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41598-017-01617-3","article-title":"Benchmarking of RNA-sequencing analysis workflows using whole transcriptome RT-qPCR expression data","volume":"7","author":"Everaert","year":"2017","journal-title":"Sci. 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