08-reactome.Rmd

# Reactome pathway analysis {#chapter8}

```{r include=FALSE}
library(knitr)
opts_chunk$set(message=FALSE, warning=FALSE, eval=TRUE, echo=TRUE, cache=TRUE)
library(clusterProfiler)
```


[ReactomePA](https://www.bioconductor.org/packages/ReactomePA)[@yu_reactomepa_2016] uses Reactome as a source of pathway data. The function call of `enrichPathway` and `gsePathway` in [ReactomePA](https://www.bioconductor.org/packages/ReactomePA) is consistent with `enrichKEGG` and `gseKEGG`.