CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.

Copy number variation (CNV) is a major type of structural genomic variation that is increasingly studied acrossdifferent species for association with diseases and production traits. Established protocols for experimental detection andcomputational inference of CNVs from SNP array and next-generation sequencing data are available. We present theCNVRangerR/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis ofCNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with func-tional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes.

Bibliographic Details

Main Authors:	SILVA, V. da, RAMOS, M., GROENEN, M., CROOIJMANS, R., JOHANSSON, A., REGITANO, L. C. de A., COUTINHO, L., ZIMMER, R., WALDRON, L., GEISTLINGER, L.
Other Authors:	Vinicius da Silva, Wageningen University and Research; Marcel Ramos, Swedish University of Agricultural Sciences; Martien Groenen, Wageningen University and Research; Richard Crooijmans, Wageningen University and Research; Anna Johansson, Swedish University of Agricultural Sciences; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; Luiz Coutinho, USP; Ralf Zimmer, Universität München; Levi Waldron, University of New York; Ludwig Geistlinger, University of New York.
Format:	Artigo de periódico biblioteca
Language:	Ingles English
Published:	2019-11-29
Subjects:	Genomic hybridization, Structural genomic, Expressão gênica, Fenótipos quantitativos, Quantitative phenotypes,
Online Access:	http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115536
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