README.md

In funnell/reactomefi: Reactome FI network analysis tools

Reactome-FI

R Reactome FI Cytoscape plugin wrapper. This package currently implements a limited interface to ReactomeFI functionality including network construction, network clustering, and Pathway/GO term enrichment. It also implements some network plotting capabilities using either sna/ggplot2 or RCytoscape.

Dependencies

• plyr
• ggplot2
• sna
• RCurl
• XML

Installation

The easiest way to install reactomefi is through devtools:

devtools::install_github("funnell/reactomefi")

Get Started:

network <- ReactomeFINetwork("2012", genes)
annotate(network, "Pathway")
plot(network)

network <- ReactomeFINetwork("2012", genes, cluster=TRUE)
annotateModules(network, "Pathway")
plot(network)

funnell/reactomefi documentation built on May 16, 2019, 4:05 p.m.