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ensembldb: an R package to create and use Ensembl-based annotation resources
SUMMARY: Bioinformatics research frequently involves handling gene-centric data such as exons, transcripts, proteins and their positions relative to a reference coordinate system. The ensembldb Bioconductor package retrieves and stores Ensembl-based genetic annotations and positional information, an...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736197/ https://www.ncbi.nlm.nih.gov/pubmed/30689724 http://dx.doi.org/10.1093/bioinformatics/btz031 |
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author | Rainer, Johannes Gatto, Laurent Weichenberger, Christian X |
author_facet | Rainer, Johannes Gatto, Laurent Weichenberger, Christian X |
author_sort | Rainer, Johannes |
collection | PubMed |
description | SUMMARY: Bioinformatics research frequently involves handling gene-centric data such as exons, transcripts, proteins and their positions relative to a reference coordinate system. The ensembldb Bioconductor package retrieves and stores Ensembl-based genetic annotations and positional information, and furthermore offers identifier conversion and coordinates mappings for gene-associated data. In support of reproducible research, data are tied to Ensembl releases and are kept separately from the software. Premade data packages are available for a variety of genomes and Ensembl releases. Three examples demonstrate typical use cases of this software. AVAILABILITY AND IMPLEMENTATION: ensembldb is part of Bioconductor (https://bioconductor.org/packages/ensembldb). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-6736197 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-67361972019-09-16 ensembldb: an R package to create and use Ensembl-based annotation resources Rainer, Johannes Gatto, Laurent Weichenberger, Christian X Bioinformatics Applications Notes SUMMARY: Bioinformatics research frequently involves handling gene-centric data such as exons, transcripts, proteins and their positions relative to a reference coordinate system. The ensembldb Bioconductor package retrieves and stores Ensembl-based genetic annotations and positional information, and furthermore offers identifier conversion and coordinates mappings for gene-associated data. In support of reproducible research, data are tied to Ensembl releases and are kept separately from the software. Premade data packages are available for a variety of genomes and Ensembl releases. Three examples demonstrate typical use cases of this software. AVAILABILITY AND IMPLEMENTATION: ensembldb is part of Bioconductor (https://bioconductor.org/packages/ensembldb). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2019-09-01 2019-01-25 /pmc/articles/PMC6736197/ /pubmed/30689724 http://dx.doi.org/10.1093/bioinformatics/btz031 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Rainer, Johannes Gatto, Laurent Weichenberger, Christian X ensembldb: an R package to create and use Ensembl-based annotation resources |
title | ensembldb: an R package to create and use Ensembl-based annotation resources |
title_full | ensembldb: an R package to create and use Ensembl-based annotation resources |
title_fullStr | ensembldb: an R package to create and use Ensembl-based annotation resources |
title_full_unstemmed | ensembldb: an R package to create and use Ensembl-based annotation resources |
title_short | ensembldb: an R package to create and use Ensembl-based annotation resources |
title_sort | ensembldb: an r package to create and use ensembl-based annotation resources |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736197/ https://www.ncbi.nlm.nih.gov/pubmed/30689724 http://dx.doi.org/10.1093/bioinformatics/btz031 |
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