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

Detalhes bibliográficos
Autor(a) principal: SILVA, V. da
Data de Publicação: 2019
Outros Autores: RAMOS, M., GROENEN, M., CROOIJMANS, R., JOHANSSON, A., REGITANO, L. C. de A., COUTINHO, L., ZIMMER, R., WALDRON, L., GEISTLINGER, L.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115536
Resumo: 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.
id EMBR_dedcec443b39df2b0beb16aa5f9f7542
oai_identifier_str oai:www.alice.cnptia.embrapa.br:doc/1115536
network_acronym_str EMBR
network_name_str Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository_id_str 2154
spelling CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.Genomic hybridizationStructural genomicExpressão gênicaFenótipos quantitativosQuantitative phenotypesCopy 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.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.SILVA, V. daRAMOS, M.GROENEN, M.CROOIJMANS, R.JOHANSSON, A.REGITANO, L. C. de A.COUTINHO, L.ZIMMER, R.WALDRON, L.GEISTLINGER, L.2020-12-04T09:01:06Z2020-12-04T09:01:06Z2019-11-292020info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleBioinformatics, v. 36, n. 3, p. 972-973, 2020.http://www.alice.cnptia.embrapa.br/alice/handle/doc/111553610.1093/bioinformatics/btz632enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2020-12-04T09:01:18Zoai:www.alice.cnptia.embrapa.br:doc/1115536Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542020-12-04T09:01:18Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
title CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
spellingShingle CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
SILVA, V. da
Genomic hybridization
Structural genomic
Expressão gênica
Fenótipos quantitativos
Quantitative phenotypes
title_short CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
title_full CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
title_fullStr CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
title_full_unstemmed CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
title_sort CNVRanger: association analysis of CNVs with geneexpression and quantitative phenotypes.
author SILVA, V. da
author_facet SILVA, V. da
RAMOS, M.
GROENEN, M.
CROOIJMANS, R.
JOHANSSON, A.
REGITANO, L. C. de A.
COUTINHO, L.
ZIMMER, R.
WALDRON, L.
GEISTLINGER, L.
author_role author
author2 RAMOS, M.
GROENEN, M.
CROOIJMANS, R.
JOHANSSON, A.
REGITANO, L. C. de A.
COUTINHO, L.
ZIMMER, R.
WALDRON, L.
GEISTLINGER, L.
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv 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.
dc.contributor.author.fl_str_mv SILVA, V. da
RAMOS, M.
GROENEN, M.
CROOIJMANS, R.
JOHANSSON, A.
REGITANO, L. C. de A.
COUTINHO, L.
ZIMMER, R.
WALDRON, L.
GEISTLINGER, L.
dc.subject.por.fl_str_mv Genomic hybridization
Structural genomic
Expressão gênica
Fenótipos quantitativos
Quantitative phenotypes
topic Genomic hybridization
Structural genomic
Expressão gênica
Fenótipos quantitativos
Quantitative phenotypes
description 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.
publishDate 2019
dc.date.none.fl_str_mv 2019-11-29
2020-12-04T09:01:06Z
2020-12-04T09:01:06Z
2020
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv Bioinformatics, v. 36, n. 3, p. 972-973, 2020.
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115536
10.1093/bioinformatics/btz632
identifier_str_mv Bioinformatics, v. 36, n. 3, p. 972-973, 2020.
10.1093/bioinformatics/btz632
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115536
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron:EMBRAPA
instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron_str EMBRAPA
institution EMBRAPA
reponame_str Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository.name.fl_str_mv Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
repository.mail.fl_str_mv cg-riaa@embrapa.br
_version_ 1822721499953364992

Registros relacionados