{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:37Z","timestamp":1740185137151,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,3,14]],"date-time":"2020-03-14T00:00:00Z","timestamp":1584144000000},"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\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["31500674","31801084"],"award-info":[{"award-number":["31500674","31801084"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NJU-Yangzhou Institute of Optoelectronics"},{"name":"National Science and Technology Major Project of China","award":["2015ZX09102023-003"],"award-info":[{"award-number":["2015ZX09102023-003"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The R\/Bioconductor package primirTSS is a fast and convenient tool that allows implementation of the analytical method to identify transcription start sites of microRNAs by integrating ChIP-seq data of H3K4me3 and Pol II. It further ensures the precision by employing the conservation score and sequence features. The tool showed a good performance when using H3K4me3 or Pol II Chip-seq data alone as input, which brings convenience to applications where multiple datasets are hard to acquire. This flexible package is provided with both R-programming interfaces as well as graphical web interfaces.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>primirTSS is available at: http:\/\/bioconductor.org\/packages\/primirTSS. The documentation of the package including an accompanying tutorial was deposited at: https:\/\/bioconductor.org\/packages\/release\/bioc\/vignettes\/primirTSS\/inst\/doc\/primirTSS.html.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>jwang@nju.edu.cn<\/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\/btaa173","type":"journal-article","created":{"date-parts":[[2020,3,10]],"date-time":"2020-03-10T12:35:32Z","timestamp":1583843732000},"page":"3605-3606","source":"Crossref","is-referenced-by-count":1,"title":["primirTSS: an R package for identifying cell-specific microRNA transcription start sites"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4803-1346","authenticated-orcid":false,"given":"Pumin","family":"Li","sequence":"first","affiliation":[{"name":"The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology , NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210093, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Xu","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology , NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210093, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9775-4129","authenticated-orcid":false,"given":"Xu","family":"Hua","sequence":"additional","affiliation":[{"name":"High-Tech Research Institute of Nanjing University , Changzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongwei","family":"Xie","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology , NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210093, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Li","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology , NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210093, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin","family":"Wang","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology , NJU Advanced Institute for Life Sciences (NAILS), School of Life Science, Nanjing University, Nanjing 210093, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,3,14]]},"reference":[{"key":"2023062312021357600_btaa173-B1","doi-asserted-by":"crossref","first-page":"9345","DOI":"10.1093\/nar\/gkr604","article-title":"Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data","volume":"39","author":"Chien","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023062312021357600_btaa173-B2","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1101\/gr.216102","article-title":"Computational detection and location of transcription start sites in mammalian genomic DNA","volume":"12","author":"Down","year":"2002","journal-title":"Genome Res"},{"key":"2023062312021357600_btaa173-B3","doi-asserted-by":"crossref","first-page":"5700.","DOI":"10.1038\/ncomms6700","article-title":"microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs","volume":"5","author":"Georgakilas","year":"2014","journal-title":"Nat. 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