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Reactome-FI

Build Status

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)