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. Supplementary information Supplementary data are available at Bioinformatics online.