Associate Editor1 B2SLab, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Barcelona, Spain2 Department of Biomedical Engineering, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain3 Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Roskilde, Denmark4 Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, USA
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SummaryLabel 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 implementationThe R package diffuStats is publicly available in Bioconductor, https://bioconductor.org, under the GPL-3 license.