Rainer Johannes, Gatto Laurent, Weichenberger Christian X
Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
de Duve Institute, UCLouvain, Brussels, Belgium.
Bioinformatics. 2019 Sep 1;35(17):3151-3153. doi: 10.1093/bioinformatics/btz031.
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.
ensembldb is part of Bioconductor (https://bioconductor.org/packages/ensembldb).
Supplementary data are available at Bioinformatics online.
生物信息学研究经常涉及处理以基因为中心的数据，例如外显子、转录本、蛋白质及其相对于参考坐标系的位置。ensembldb Bioconductor软件包检索并存储基于Ensembl的遗传注释和位置信息，此外还为基因相关数据提供标识符转换和坐标映射。为支持可重复研究，数据与Ensembl版本相关联，并与软件分开保存。针对多种基因组和Ensembl版本提供了预制数据包。三个示例展示了该软件的典型用例。
ensembldb是Bioconductor的一部分(https://bioconductor.org/packages/ensembldb)。
补充数据可在《生物信息学》在线版获取。
