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Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R\/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>http:\/\/bioconductor.org\/packages\/CNVRanger.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz632","type":"journal-article","created":{"date-parts":[[2019,8,6]],"date-time":"2019-08-06T19:17:18Z","timestamp":1565119038000},"page":"972-973","source":"Crossref","is-referenced-by-count":33,"title":["CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4368-812X","authenticated-orcid":false,"given":"Vinicius","family":"da Silva","sequence":"first","affiliation":[{"name":"Department of Animal Breeding and Genomics, Wageningen University and Research , 6708 PB Wageningen, The Netherlands"},{"name":"Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala 75007, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcel","family":"Ramos","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York , New York, NY 10027, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martien","family":"Groenen","sequence":"additional","affiliation":[{"name":"Department of Animal Breeding and Genomics, Wageningen University and Research , 6708 PB Wageningen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Crooijmans","sequence":"additional","affiliation":[{"name":"Department of Animal Breeding and Genomics, Wageningen University and Research , 6708 PB Wageningen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Johansson","sequence":"additional","affiliation":[{"name":"Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala 75007, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciana","family":"Regitano","sequence":"additional","affiliation":[{"name":"Embrapa Pecuaria Sudeste , 13560-970 S\u00e3o Carlos, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz","family":"Coutinho","sequence":"additional","affiliation":[{"name":"Department of Animal Science, University of S\u00e3o Paulo , 13418-900 Piracicaba, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralf","family":"Zimmer","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, 80333 M\u00fcnchen , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2725-0694","authenticated-orcid":false,"given":"Levi","family":"Waldron","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York , New York, NY 10027, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2495-5464","authenticated-orcid":false,"given":"Ludwig","family":"Geistlinger","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York , New York, NY 10027, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,8]]},"reference":[{"key":"2023013110074655400_btz632-B1","doi-asserted-by":"crossref","first-page":"20007","DOI":"10.1073\/pnas.0710052104","article-title":"Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma","volume":"104","author":"Beroukhim","year":"2007","journal-title":"Proc. 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