NOTE: Users interested in the source code should download the code directly from Bioconductor repositories:

• Release Version
• Development Version

PaxtoolsR

An R package providing Paxtools and Pathway Commons functionality. This project provides users with the ability to read BioPAX files and access Pathway Commons web service functions to:

• Merge multiple BioPAX files
• Extract sub-networks from BioPAX files
• Do a number of format conversions
• Validate BioPAX files
• Search and retrieve Pathway Commons data

This package is primarily directed towards R users who wish to work with binary interactions networks in the form of Simple Interaction Format (SIF) networks.

Install PaxtoolsR from Bioconductor (Recommended)

Dependencies

Windows (tested on Windows 10)

Java needs to be installed. NOTE: If using a 64-bit system, make sure to install (or re-install) the 64-bit version. Otherwise, you may encounter an rJava issue with JAVA_HOME.

• NOTE: Installation on Windows 10 from GitHub using devtools::install_github may require args="--no-multiarch"

OS X (tested on Mavericks OSX 10.9+)

Java needs to be installed. If it is not installed, you will be prompted to install Java the first time you load the paxtoolsr package (NOTE: This prompt may crash RStudio, but installation of Java should not be affected).

• NOTE: Further instructions on rJava installation are found here: http://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite

Ubuntu (tested on Ubuntu 14.04)

Run these commands in the Terminal:

# For latest R version
sudo apt-add-repository -y ppa:marutter/rrutter
sudo apt-get -y update
sudo apt-get -y upgrade
sudo apt-get -y install r-base
# For plyr
sudo apt-get -y install g++
# For RCurl
sudo apt-get -y install libcurl4-openssl-dev
# For rJava
sudo apt-get -y install liblzma-dev
sudo apt-get -y install libbz2-dev
sudo apt-get -y install libpcre++-dev
sudo apt-get -y install openjdk-7-jdk  
# For XML
sudo apt-get -y install libxml2-dev
# To let R find Java
sudo R CMD javareconf

Install Bioconductor and PaxtoolsR

Run these commands within R:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("paxtoolsr") 

Install PaxtoolsR Development Version from GitHub

setRepositories(ind=1:6)
options(repos="http://cran.rstudio.com/")
if(!require(remotes)) { install.packages("remotes") }
library(remotes) 

remotes::install_github("BioPAX/paxtoolsr")
remotes::install_github("BioPAX/paxtoolsr", args="--no-multiarch") # On Windows, 64-bit

Using PaxtoolsR: R Vignette (Tutorial)

The tutorial describes a number of possible use cases, including network visualization and gene set enrichment analysis using this R package. Once installed, view tutorials for PaxtoolsR using the following command:

library(paxtoolsr)
browseVignettes("paxtoolsr")

A copy of the vignette Using PaxtoolsR is viewable from the Bioconductor website.