CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies

Biomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R/Bioconductor projects provide several tools for performing enrichment analysis at gene-pathway level, allowing researchers to develop novel hypotheses. However, the...

Descripción completa

Detalles Bibliográficos
Autores: Hernández Ferrer, Carles, González, Juan R.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2018
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/125247
Acceso en línea:https://hdl.handle.net/2445/125247
Access Level:acceso abierto
Palabra clave:Ciències de la salut
Etiologia
Medical sciences
Etiology
id ES_14b2701385a2ca02ea936bafa58f2521
oai_identifier_str oai:recercat.cat:2445/125247
network_acronym_str ES
network_name_str España
repository_id_str
spelling CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studiesHernández Ferrer, CarlesGonzález, Juan R.Ciències de la salutEtiologiaMedical sciencesEtiologyBiomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R/Bioconductor projects provide several tools for performing enrichment analysis at gene-pathway level, allowing researchers to develop novel hypotheses. However, there is a need to perform similar analyses at the chemicals-genes or chemicals-diseases levels, to provide complementary knowledge of the causal path between chemicals and diseases. While the Comparative Toxicogenomics DatabaseTM (CTD) provides information about these relationships, there is no software for integrating it into R/Bioconductor analysis pipelines. CTDquerier helps users to easily download CTD data and integrate it in the R/Bioconductor framework. The package also contains functions for visualizing CTD data and performing enrichment analyses. We illustrate how to use the package with a real data analysis of asthma-related genes. CTDquerier is a flexible and easy-to-use Bioconductor package that provides novel hypothesis about the relationships between chemicals and diseases. Availability and implementation: CTDquerier R package is available through Bioconductor and its development version at https://github.com/isglobal-brge/CTDquerier. Contact: juanr.gonzalez@isglobal.org. Supplementary information: Supplementary data are available at Bioinformatics online.Oxford University Press2018201820182018info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion3 p.application/pdfapplication/pdfhttps://hdl.handle.net/2445/125247Articles publicats en revistes (ISGlobal)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: http://dx.doi.org/10.1093/bioinformatics/bty326Bioinformatics, 2018, vol. 34, num. 18, p. 3235–3237http://dx.doi.org/10.1093/bioinformatics/bty326info:eu-repo/grantAgreement/EC/FP7/308333cc by-nc (c) Hernández Ferrer, Carles; González, Juan R., 2018http://creativecommons.org/licenses/by-nc/3.0/es/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1252472026-05-29T05:05:01Z
dc.title.none.fl_str_mv CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
spellingShingle CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
Hernández Ferrer, Carles
Ciències de la salut
Etiologia
Medical sciences
Etiology
title_short CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_full CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_fullStr CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_full_unstemmed CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_sort CTDquerier: A Bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
dc.creator.none.fl_str_mv Hernández Ferrer, Carles
González, Juan R.
author Hernández Ferrer, Carles
author_facet Hernández Ferrer, Carles
González, Juan R.
author_role author
author2 González, Juan R.
author2_role author
dc.subject.none.fl_str_mv Ciències de la salut
Etiologia
Medical sciences
Etiology
topic Ciències de la salut
Etiologia
Medical sciences
Etiology
description Biomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R/Bioconductor projects provide several tools for performing enrichment analysis at gene-pathway level, allowing researchers to develop novel hypotheses. However, there is a need to perform similar analyses at the chemicals-genes or chemicals-diseases levels, to provide complementary knowledge of the causal path between chemicals and diseases. While the Comparative Toxicogenomics DatabaseTM (CTD) provides information about these relationships, there is no software for integrating it into R/Bioconductor analysis pipelines. CTDquerier helps users to easily download CTD data and integrate it in the R/Bioconductor framework. The package also contains functions for visualizing CTD data and performing enrichment analyses. We illustrate how to use the package with a real data analysis of asthma-related genes. CTDquerier is a flexible and easy-to-use Bioconductor package that provides novel hypothesis about the relationships between chemicals and diseases. Availability and implementation: CTDquerier R package is available through Bioconductor and its development version at https://github.com/isglobal-brge/CTDquerier. Contact: juanr.gonzalez@isglobal.org. Supplementary information: Supplementary data are available at Bioinformatics online.
publishDate 2018
dc.date.none.fl_str_mv 2018
2018
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/125247
url https://hdl.handle.net/2445/125247
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: http://dx.doi.org/10.1093/bioinformatics/bty326
Bioinformatics, 2018, vol. 34, num. 18, p. 3235–3237
http://dx.doi.org/10.1093/bioinformatics/bty326
info:eu-repo/grantAgreement/EC/FP7/308333
dc.rights.none.fl_str_mv cc by-nc (c) Hernández Ferrer, Carles; González, Juan R., 2018
http://creativecommons.org/licenses/by-nc/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc by-nc (c) Hernández Ferrer, Carles; González, Juan R., 2018
http://creativecommons.org/licenses/by-nc/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 3 p.
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv Articles publicats en revistes (ISGlobal)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869403751269269504
score 15.81155

Similares en LA Referencia