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![R-CMD-check]( **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: #### 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="") 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]( is viewable from the Bioconductor website.