CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

Bioinformatics
Vinicius Henrique da SilvaLudwig Geistlinger

Abstract

Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. 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. http://bioconductor.org/packages/CNVRanger.

References

Dec 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Rameen BeroukhimWilliam R Sellers
Oct 9, 2009·Nature·Donald F ConradMatthew E Hurles
Apr 28, 2012·Bioinformatics·Ji-Hong KimYeun-Jun Chung
Aug 21, 2013·PLoS Computational Biology·Michael LawrenceVincent J Carey
Jan 31, 2015·Nature Methods·Wolfgang HuberMartin Morgan
Jun 28, 2016·PloS One·Vinicius Henrique da SilvaLuiz Lehmann Coutinho
Jan 25, 2018·Scientific Reports·Ludwig GeistlingerLuiz Lehmann Coutinho
Apr 29, 2018·BMC Genomics·Vinicius H da SilvaMartien A M Groenen

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Citations

May 19, 2021·BMC Genomics·Anna Carolina FernandesLuiz Lehmann Coutinho

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