aMatReader: Importing adjacency matrices via Cytoscape Automation [version 2; referees: 2 approved]

• Main Authors: Brett Settle, David Otasek, John H Morris, Barry Demchak
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2018-08-01
• Series: F1000Research
• Online Access: https://f1000research.com/articles/7-823/v2

Adjacency matrices are useful for storing pairwise interaction data, such as correlations between gene pairs in a pathway or similarities between genes and conditions. The aMatReader app enables users to import one or multiple adjacency matrix files into Cytoscape, where each file represents an edge attribute in a network. Our goal was to import the diverse adjacency matrix formats produced by existing scripts and libraries written in R, MATLAB, and Python, and facilitate importing that data into Cytoscape. To accelerate the import process, aMatReader attempts to predict matrix import parameters by analyzing the first two lines of the file. We also exposed CyREST endpoints to allow researchers to import network matrix data directly into Cytoscape from their language of choice. Many analysis tools deal with networks in the form of an adjacency matrix, and exposing the aMatReader API to automation users enables scripts to transfer those networks directly into Cytoscape with little effort.