CausalR - extracting mechanistic sense from genome scale data

Abstract

Summary: Utilization of causal interaction data enables mechanistic rather than descriptive interpretation of genome scale data. Here we present CausalR, the first open source causal network analysis platform. Implemented functions enable regulator prediction and network reconstruction, with network and annotation files created for visualisation in Cytoscape. False positives are limited using the introduced SCAN (Sequential Causal Analysis of Networks) approach.

Implementation and Availability: CausalR is implemented in R, parallelised, and is available from Bioconductor.

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Supplementary information:Supplementary information and data, including a substrate causal network, is available at bioinformatics online. A detailed vignette is included in the Bioconductor package.

Author notes

Associate Editor: Dr. Janet Kelso