**NOTE:** Users interested in the source code should download the code directly from Bioconductor repositories:
* [Release Version](http://bioconductor.org/packages/devel/bioc/html/paxtoolsr.html)
* [Development Version](http://bioconductor.org/packages/devel/bioc/html/paxtoolsr.html)
# PaxtoolsR
An R package providing [Paxtools](http://www.biopax.org/paxtools.php) and [Pathway Commons](http://www.pathwaycommons.org/) 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](http://www.oracle.com/technetwork/java/javase/downloads/index.html) 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](http://www.r-statistics.com/2012/08/how-to-load-the-rjava-package-after-the-error-java_home-cannot-be-determined-from-the-registry/).
* 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(devtools)) { install.packages("devtools") }
library(devtools)
install_github("BioPAX/paxtoolsr")
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](http://bioconductor.org/packages/release/bioc/vignettes/paxtoolsr/inst/doc/using_paxtoolsr.html) is viewable from the Bioconductor website.
