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clusterProfiler 4.0：用于解释组学数据的通用富集工具。

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.

作者信息

Wu Tianzhi, Hu Erqiang, Xu Shuangbin, Chen Meijun, Guo Pingfan, Dai Zehan, Feng Tingze, Zhou Lang, Tang Wenli, Zhan Li, Fu Xiaocong, Liu Shanshan, Bo Xiaochen, Yu Guangchuang

机构信息

Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.

Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.

出版信息

Innovation (Camb). 2021 Jul 1;2(3):100141. doi: 10.1016/j.xinn.2021.100141. eCollection 2021 Aug 28.

DOI:10.1016/j.xinn.2021.100141
PMID:34557778
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8454663/
Abstract

Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible. To meet these requirements, we present here an updated version of our popular Bioconductor package, clusterProfiler 4.0. This package has been enhanced considerably compared with its original version published 9 years ago. The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases. It also extends the and packages to offer tidy interfaces for data operation and visualization. Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists. We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.

摘要

功能富集分析对于解释生命科学中的高通量组学数据至关重要。对于这类工具而言，尽可能多地使用最新注释数据库来涵盖多种生物至关重要。为满足这些要求，我们在此展示我们广受欢迎的Bioconductor软件包clusterProfiler 4.0的更新版本。与9年前发布的原始版本相比，该软件包有了显著增强。新版本基于内部支持的本体和通路以及用户提供或从在线数据库派生的注释数据，为数千种生物的功能富集分析提供了通用接口。它还扩展了 和 软件包，以提供用于数据操作和可视化的简洁接口。其他新功能包括基因集富集分析以及多个基因列表富集结果的比较。我们预计clusterProfiler 4.0将应用于跨多种生物的广泛场景。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/ab1696f2e75e/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/47349bb5659e/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/b73d24a90df4/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/6165fc242456/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/58f650eead56/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/84eacf0856e0/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/1395c50b3ef8/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/ab1696f2e75e/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/47349bb5659e/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/b73d24a90df4/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/6165fc242456/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/58f650eead56/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/84eacf0856e0/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/1395c50b3ef8/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ff8/8454663/ab1696f2e75e/gr6.jpg

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