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README.md
# Welcome to RCy3: 2.0 and Beyond Building upon the phenominal success of RCytoscape and RCy3, Cytoscape is adopting the project (and primary responsibility) to provide a robust R package for the rapidly evolving Cytoscape ecosystem. We are beginning with a major refactor of RCy3 that includes: * independence from the graphNEL object model * optional object-based arguments * harmonized function and argument names * support for Cytoscape commands * better support for Cytoscape apps * coordinated development with CyREST and the Cytoscape service model * [New API](https://github.com/cytoscape/cyREST/issues?utf8=✓&q=milestone%3A*+label%3A%22new+API%22+is%3A*) * coordinated development with other scripting libraries, e.g., * [py2cytoscape](https://github.com/cytoscape/py2cytoscape) * [RCyjs](http://bioconductor.org/packages/release/bioc/html/RCyjs.html) ## How to install **_Official bioconductor releases_ (recommended)** ``` source("https://bioconductor.org/biocLite.R") biocLite("RCy3") ``` _Unstable development code from this repo_ (at your own risk) ``` install_github('cytoscape/RCy3') library(RCy3) ``` ## How to contribute This is a public, open source project. Come on in! You can contribute at multiple levels: * Report an issue or feature request * Fork and make pull requests * Contact current Cytoscape developers and inquire about joining the team ## Testing Unit tests are a crucial tool in software development. In order to run them 'offline' (not on the Bioconductor build system), take these steps from within a running R session: 1) source(system.file("unitTests", "test_RCy3.R", package="RCy3")) 2) run.tests () They take about 4 minutes to run. ## Bioconductor While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository ([devel](http://bioconductor.org/packages/devel/bioc/html/RCy3.html) & [release](http://bioconductor.org/packages/release/bioc/html/RCy3.html)) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `master` branch here corresponds to the latest code in development and not yet released. ## Former Repo The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier at https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape.