Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany.
Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg 69120, Germany.
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac745.
GREAT (Genomic Regions Enrichment of Annotations Tool) is a widely used tool for functional enrichment on genomic regions. However, as an online tool, it has limitations of outdated annotation data, small numbers of supported organisms and gene set collections, and not being extensible for users. Here, we developed a new R/Bioconductorpackage named rGREAT which implements the GREAT algorithm locally. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.
The package rGREAT is freely available from the Bioconductor project: https://bioconductor.org/packages/rGREAT/. The development version is available at https://github.com/jokergoo/rGREAT. Gene Ontology gene sets for more than 600 organisms retrieved from Ensembl BioMart are presented in an R package BioMartGOGeneSets which is available at https://github.com/jokergoo/BioMartGOGeneSets.
Supplementary data are available at Bioinformatics online.
GREAT（基因组区域注释富集工具）是一个广泛应用于基因组区域功能富集的工具。然而，作为一个在线工具，它存在注释数据过时、支持的生物种类和基因集数量有限以及不可扩展等问题。在这里，我们开发了一个名为 rGREAT 的新的 R/Bioconductor 包，它在本地实现了 GREAT 算法。rGREAT 默认支持超过 600 种生物和大量的基因集集，以及用户提供的自定义基因集和生物。此外，它还实现了一种处理背景区域的通用方法。
rGREAT 包可从 Bioconductor 项目免费获得：https://bioconductor.org/packages/rGREAT/。开发版本可在 https://github.com/jokergoo/rGREAT 获得。从 Ensembl BioMart 检索到的超过 600 种生物的基因本体基因集以 R 包 BioMartGOGeneSets 的形式呈现，该 R 包可在 https://github.com/jokergoo/BioMartGOGeneSets 获得。
补充数据可在 Bioinformatics 在线获得。
