diffuStats: an R package to compute diffusion-based scores on biological networks

Abstract

Summary: Label propagation and diffusion over biological networks are a common mathematical formalism in computational biology for giving context to molecular entities and prioritizing novel candidates in the area of study. There are several choices in conceiving the diffusion process-involving the graph kernel, the score definitions and the presence of a posterior statistical normalization-which have an impact on the results. This manuscript describes diffuStats, an R package that provides a collection of graph kernels and diffusion scores, as well as a parallel permutation analysis for the normalized scores, that eases the computation of the scores and their benchmarking for an optimal choice.

Availability and implementation: The R package diffuStats is publicly available in Bioconductor, https://bioconductor.org, under the GPL-3 license.

Contact: sergi.picart@upc.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.