# ReactomePA: Reactome Pathway Analysis
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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!