{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T02:17:37Z","timestamp":1778811457408,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genetic screens by CRISPR\/Cas9-mediated genome engineering have become a powerful tool for functional genomics. However, there is currently a lack of end-to-end software pipelines to analyze CRISPR\/Cas9 screens based on next generation sequencing.<\/jats:p>\n               <jats:p>Results: The CRISPR-AnalyzeR for pooled screens (caRpools) is an R package for exploratory data analysis that provides a complete workflow to analyze CRISPR\/Cas9 screens. To further support the analysis of large-scale screens, caRpools integrates screening documentation and generation of standardized analysis reports.<\/jats:p>\n               <jats:p>Availability and implementation: caRpools, manuals and an open virtual appliance are available at http:\/\/github.com\/boutroslab\/caRpools.<\/jats:p>\n               <jats:p>Contact: \u00a0m.boutros@dkfz.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv617","type":"journal-article","created":{"date-parts":[[2015,10,28]],"date-time":"2015-10-28T02:38:45Z","timestamp":1445999925000},"page":"632-634","source":"Crossref","is-referenced-by-count":61,"title":["caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR\/Cas9 screens"],"prefix":"10.1093","volume":"32","author":[{"given":"Jan","family":"Winter","sequence":"first","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Breinig","sequence":"additional","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Heigwer","sequence":"additional","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Br\u00fcgemann","sequence":"additional","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Svenja","family":"Leible","sequence":"additional","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oliver","family":"Pelz","sequence":"additional","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianzuo","family":"Zhan","sequence":"additional","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"},{"name":"2 Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Boutros","sequence":"additional","affiliation":[{"name":"1 German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Heidelberg, Germany and"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,27]]},"reference":[{"key":"2023020110344148300_btv617-B1","doi-asserted-by":"crossref","first-page":"R66","DOI":"10.1186\/gb-2006-7-7-r66","article-title":"Analysis of cell-based RNAi screens","volume":"7","author":"Boutros","year":"2006","journal-title":"Genome Biol."},{"key":"2023020110344148300_btv617-B2","doi-asserted-by":"crossref","first-page":"e16","DOI":"10.1093\/nar\/gku1197","article-title":"HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis","volume":"43","author":"Diaz","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023020110344148300_btv617-B3","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nbt.2800","article-title":"Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library","volume":"32","author":"Koike-Yusa","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2023020110344148300_btv617-B4","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1186\/s13059-014-0554-4","article-title":"MAGeCK enables robust identification of essential genes from genome-scale CRISPR\/Cas9 knockout screens","volume":"15","author":"Li","year":"2014","journal-title":"Genome Biol."},{"key":"2023020110344148300_btv617-B5","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":"2023020110344148300_btv617-B6","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1038\/nbt.3291","article-title":"Flexible guide-RNA design for CRISPR applications using Protospacer Workbench","volume":"33","author":"MacPherson","year":"2015","journal-title":"Nat. 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