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README.md
# ReactomePA: Reactome Pathway Analysis [![platform](http://www.bioconductor.org/shields/availability/devel/ReactomePA.svg)](http://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ReactomePA.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomePA/) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ReactomePA.svg)](http://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#since) [![post](http://www.bioconductor.org/shields/posts/ReactomePA.svg)](https://support.bioconductor.org/t/ReactomePA/) [![commit](http://www.bioconductor.org/shields/commits/bioc/ReactomePA.svg)](http://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#svn_source) [![download](http://www.bioconductor.org/shields/downloads/ReactomePA.svg)](http://bioconductor.org/packages/stats/bioc/ReactomePA.html) This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. ## Authors ## Guangchuang YU, School of Public Health, The University of Hong Kong [http://ygc.name](http://ygc.name) ## License ## All source code is copyright, under the GPL-2 License. For more information on GPL-2 License see [http://www.gnu.org/licenses/gpl-2.0.html](http://www.gnu.org/licenses/gpl-2.0.html) ## Installation ## To install: * the latest released version: `biocLite("ReactomePA")` * the latest development version: `install_github(c("GuangchuangYu/DOSE", "GuangchuangYu/ReactomePA"))` ## Documentation ## + [Why clusterProfiler fails](http://ygc.name/2014/08/07/why-clusterprofiler-fails/) + [use clusterProfiler as an universal enrichment analysis tool](http://ygc.name/2015/05/11/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/) + [Enrichment map](http://ygc.name/2014/08/03/enrichment-map/) + [dotplot for enrichment result](http://ygc.name/2015/06/23/dotplot-for-enrichment-result/) + [functional enrichment for GTEx paper](http://ygc.name/2015/08/13/functional-enrichment-for-gtex-paper/) + [functional enrichment analysis with NGS data](http://ygc.name/2015/08/21/functional-enrichment-analysis-with-ngs-data/) To view the vignette of `ReactomePA` installed in your system, start `R` and enter: ```r vignette("ReactomePA", package="ReactomePA") ``` ## Bugs/Feature requests ## - If you have any, [let me know](https://github.com/GuangchuangYu/ReactomePA/issues). Thx!