BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA...

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Autores principales: Komljenovic, Andrea, Roux, Julien, Wollbrett, Julien, Robinson-Rechavi, Marc, Bastian, Frederic B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2018
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6113886/
https://www.ncbi.nlm.nih.gov/pubmed/30467516
http://dx.doi.org/10.12688/f1000research.9973.2
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author Komljenovic, Andrea
Roux, Julien
Wollbrett, Julien
Robinson-Rechavi, Marc
Bastian, Frederic B.
author_facet Komljenovic, Andrea
Roux, Julien
Wollbrett, Julien
Robinson-Rechavi, Marc
Bastian, Frederic B.
author_sort Komljenovic, Andrea
collection PubMed
description BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures (“TopAnat”). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability: https://www.bioconductor.org/packages/BgeeDB/
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spelling pubmed-61138862018-11-21 BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests Komljenovic, Andrea Roux, Julien Wollbrett, Julien Robinson-Rechavi, Marc Bastian, Frederic B. F1000Res Software Tool Article BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures (“TopAnat”). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability: https://www.bioconductor.org/packages/BgeeDB/ F1000 Research Limited 2018-08-07 /pmc/articles/PMC6113886/ /pubmed/30467516 http://dx.doi.org/10.12688/f1000research.9973.2 Text en Copyright: © 2018 Komljenovic A et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Komljenovic, Andrea
Roux, Julien
Wollbrett, Julien
Robinson-Rechavi, Marc
Bastian, Frederic B.
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
title BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
title_full BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
title_fullStr BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
title_full_unstemmed BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
title_short BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
title_sort bgeedb, an r package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6113886/
https://www.ncbi.nlm.nih.gov/pubmed/30467516
http://dx.doi.org/10.12688/f1000research.9973.2
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