RCX – an R package adapting the Cytoscape Exchange format for biological networks

Author:

Auer FlorianORCID,Kramer FrankORCID

Abstract

AbstractMotivationThe Cytoscape Exchange (CX) format is a JSON-based data structure designed for the transmission of biological networks using standard web technologies. It was developed by the network data exchange (NDEx), which itself serves as online commons to share and collaborate on biological networks. The Cytoscape software for the analysis and visualization of biological networks contributes further elements to capture the visual layout within the CX format. However, there is a fundamental difference between web standards and R of how data has to be structured.ResultsHere we present a software package to create, handle, validate, visualize and convert networks in CX format to standard data types and objects within R. Networks in this format can serve as a source for biological knowledge, and also capture the results of the analysis of those while preserving the visual layout across all platforms. The RCX package connects the R environment for statistical computing with platforms for collaboration, analysis and visualization of biological networks.AvailabilityRCX is a free and open-source R package, available via GitHub (https://github.com/frankkramer-lab/RCX) and submitted to Bioconductor.Contactflorian.auer@informatik.uni-augsburg.deSupplementary informationSupplementary data are available at Bioinformatics online.

Publisher

Cold Spring Harbor Laboratory

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