{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:20:56Z","timestamp":1761920456552,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2018,5,22]],"date-time":"2018-05-22T00:00:00Z","timestamp":1526947200000},"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\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P01CA142538","5P50-CA190991-04"],"award-info":[{"award-number":["P01CA142538","5P50-CA190991-04"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error. The algorithm uses a Trie data structure for speed and resolves ambiguous mappings by using a statistical sequencing error model based on Phred scores for each read.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The package source code and an accompanying tutorial are available at http:\/\/bioconductor.org\/packages\/bcSeq\/.<\/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\/bty402","type":"journal-article","created":{"date-parts":[[2018,5,15]],"date-time":"2018-05-15T03:12:51Z","timestamp":1526353971000},"page":"3581-3583","source":"Crossref","is-referenced-by-count":3,"title":["<tt>bcSeq<\/tt>: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens"],"prefix":"10.1093","volume":"34","author":[{"given":"Jiaxing","family":"Lin","sequence":"first","affiliation":[{"name":"Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA"}]},{"given":"Jeremy","family":"Gresham","sequence":"additional","affiliation":[{"name":"Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA"}]},{"given":"Tongrong","family":"Wang","sequence":"additional","affiliation":[{"name":"Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA"}]},{"given":"So Young","family":"Kim","sequence":"additional","affiliation":[{"name":"Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA"}]},{"given":"James","family":"Alvarez","sequence":"additional","affiliation":[{"name":"Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA"},{"name":"Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA"}]},{"given":"Jeffrey S","family":"Damrauer","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"}]},{"given":"Scott","family":"Floyd","sequence":"additional","affiliation":[{"name":"Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA"},{"name":"Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA"},{"name":"Radiation Oncology, Duke University Medical Center, Durham, NC, USA"}]},{"given":"Joshua","family":"Granek","sequence":"additional","affiliation":[{"name":"Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Center for Statistical Genetics and Genomics, Duke University Medical Center, Durham, NC, USA"}]},{"given":"Andrew","family":"Allen","sequence":"additional","affiliation":[{"name":"Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Center for Statistical Genetics and Genomics, Duke University Medical Center, Durham, NC, USA"}]},{"given":"Cliburn","family":"Chan","sequence":"additional","affiliation":[{"name":"Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Center for Statistical Genetics and Genomics, Duke University Medical Center, Durham, NC, USA"}]},{"given":"Jichun","family":"Xie","sequence":"additional","affiliation":[{"name":"Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Center for Statistical Genetics and Genomics, Duke University Medical Center, Durham, NC, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3340-1287","authenticated-orcid":false,"given":"Kouros","family":"Owzar","sequence":"additional","affiliation":[{"name":"Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA"},{"name":"Duke Center for Statistical Genetics and Genomics, Duke University Medical Center, Durham, NC, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,5,22]]},"reference":[{"first-page":"35","year":"1994","author":"Bieganski","key":"2023012712421253800_bty402-B1"},{"key":"2023012712421253800_bty402-B2","first-page":"95","article-title":"edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens","volume":"3","author":"Dai","year":"2014","journal-title":"F1000Research"},{"key":"2023012712421253800_bty402-B3","doi-asserted-by":"crossref","first-page":"1258096","DOI":"10.1126\/science.1258096","article-title":"The 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