{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T04:17:57Z","timestamp":1684210677155},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,7,27]],"date-time":"2020-07-27T00:00:00Z","timestamp":1595808000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>RNA-sequencing (RNA-Seq) is the current method of choice for studying bacterial transcriptomes. To date, many computational pipelines have been developed to predict differentially expressed genes from RNA-Seq data, but no gold-standard has been widely accepted. We present the Snakemake-based tool Smart Consensus Of RNA Expression (SCORE) which uses a consensus approach founded on a selection of well-established tools for differential gene expression analysis. This allows SCORE to increase the overall prediction accuracy and to merge varying results into a single, human-readable output. SCORE performs all steps for the analysis of bacterial RNA-Seq data, from read preprocessing to the overrepresentation analysis of significantly associated ontologies. Development of consensus approaches like SCORE will help to streamline future RNA-Seq workflows and will fundamentally contribute to the creation of new gold-standards for the analysis of these types of data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/SiWolf\/SCORE.<\/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\/btaa681","type":"journal-article","created":{"date-parts":[[2020,7,24]],"date-time":"2020-07-24T11:32:22Z","timestamp":1595590342000},"page":"426-428","source":"Crossref","is-referenced-by-count":1,"title":["SCORE: Smart Consensus Of RNA Expression\u2014a consensus tool for detecting differentially expressed genes in bacteria"],"prefix":"10.1093","volume":"37","author":[{"given":"Silver A","family":"Wolf","sequence":"first","affiliation":[{"name":"Microbial Genomics, Robert Koch Institute , Berlin 13353, Germany"}]},{"given":"Lennard","family":"Epping","sequence":"additional","affiliation":[{"name":"Microbial Genomics, Robert Koch Institute , Berlin 13353, Germany"}]},{"given":"Sandro","family":"Andreotti","sequence":"additional","affiliation":[{"name":"Freie Universit\u00e4t Department of Mathematics and Computer Science, , Berlin 14195, Germany"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"Freie Universit\u00e4t Department of Mathematics and Computer Science, , Berlin 14195, Germany"}]},{"given":"Torsten","family":"Semmler","sequence":"additional","affiliation":[{"name":"Microbial Genomics, Robert Koch Institute , Berlin 13353, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,7,27]]},"reference":[{"key":"2023051603575418200_btaa681-B1","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-Seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. 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