clusterProfiler for enrichment analysis

Yu, Guangchuang, Li-Gen Wang, Yanyan Han, and Qing-Yu He. . OMICS: A Journal of Integrative Biology 16, no. 5 (May 2012): 284–287.

今天发现clusterProfiler已经有200个引用了。ESI高被引文章。发表在OMICS上，是OMICS杂志第二高引用文章。

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at 

最初才支持3个物种，只能做KEGG和GO，只支持超几何分布。

做为良心的作品，发表文章后不断更新维护，现在GSEA支持，GO支持Bioconductor上20个物种，以及可以通过AnnotationHub拉注释的很多（我也不知道到底多少）物种。KEGG在线拉数据，KEGG数据库超过5千个物种是支持的，DAVID是支持的，Broad Institute的Molecular Signatures Database也是支持的，用户自己的注释/定制注释是支持的，还可以通过结合DOSE, ReactomePA, meshes支持疾病相关的注释，Reactome通路和MeSH的分析。

现在已经被7个Bioconductor软件包depend或者import：

• :
  Interactive Multi-Omics Cancers Data Visualization and Analysis

• :
  Interactive Differential Expresion Analysis Browser

• : Engineering
  Evaluation by Gene Categorization (eegc)

• : co-expression of
  lincRNAs and protein-coding genes

• :
  Identify oncogenes and tumor suppressor genes from omics data

• :
  An R/Bioconductor package for integrative analysis with TCGA data

• :
  “TCGAbiolinksGUI: A Graphical User Interface to analyze cancer
  molecular and clinical data”

同时也被整合于一些分析流程中，比如 : An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data

还有小迷弟什么的 -,-