{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T06:13:10Z","timestamp":1775801590523,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,1,4]],"date-time":"2021-01-04T00:00:00Z","timestamp":1609718400000},"content-version":"vor","delay-in-days":3,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swedish Research Council for Environment"},{"name":"Agricultural Sciences and Spatial Planning","award":["2016-00768"],"award-info":[{"award-number":["2016-00768"]}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2019-00299"],"award-info":[{"award-number":["2019-00299"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013281","name":"JPI AMR","doi-asserted-by":"crossref","award":["JPIAMR2019-109"],"award-info":[{"award-number":["JPIAMR2019-109"]}],"id":[{"id":"10.13039\/100013281","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100020979","name":"Centre for Antibiotic Resistance Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100020979","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005760","name":"University of Gothenburg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005760","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014552","name":"Adlerbertska research foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014552","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Edla Johansson foundation"},{"name":"Swedish Cancer and Allergy"},{"name":"L\u00e4ngmanska Kulturfonden"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE\u2014Coefficient-based Analysis of Fitness by read Enrichment\u2014a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition and perform appropriate statistical testing on these fitness coefficients.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CAFE is implemented in Perl and R. The source code is freely available for download under the MIT License from https:\/\/github.com\/bengtssonpalme\/cafe and http:\/\/microbiology.se\/software\/cafe\/<\/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\/btaa1086","type":"journal-article","created":{"date-parts":[[2020,12,22]],"date-time":"2020-12-22T12:21:23Z","timestamp":1608639683000},"page":"121-122","source":"Crossref","is-referenced-by-count":10,"title":["CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data"],"prefix":"10.1093","volume":"37","author":[{"given":"Anna","family":"Abramova","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg , Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden"},{"name":"Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg , SE- 40530 Gothenburg, Sweden"}]},{"given":"Adriana","family":"Osi\u0144ska","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg , Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden"},{"name":"Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg , SE- 40530 Gothenburg, Sweden"},{"name":"Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn , 10-720 Olsztyn, Poland"}]},{"given":"Haveela","family":"Kunche","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg , Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden"},{"name":"Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg , SE- 40530 Gothenburg, Sweden"},{"name":"Programme in Infection Biology, School of Bioscience, University of Sk\u00f6vde , 541 28 Sk\u00f6vde, Sweden"}]},{"given":"Emil","family":"Burman","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg , Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden"},{"name":"Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg , SE- 40530 Gothenburg, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6528-3158","authenticated-orcid":false,"given":"Johan","family":"Bengtsson-Palme","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg , Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden"},{"name":"Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg , SE- 40530 Gothenburg, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2021,1,4]]},"reference":[{"key":"2023051510463227800_btaa1086-B1","doi-asserted-by":"crossref","first-page":"139","DOI":"10.3389\/fgene.2015.00139","article-title":"Transposon insertion mapping with PIMMS \u2013 pragmatic insertional mutation mapping system","volume":"06","author":"Blanchard","year":"2015","journal-title":"Front. 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