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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.

SUBMITTER: Picart-Armada S

PROVIDER: S-EPMC5860365 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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

Picart-Armada Sergio S Thompson Wesley K WK Buil Alfonso A Perera-Lluna Alexandre A

Bioinformatics (Oxford, England) 20180201 3

<h4>Summary</h4>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 provid ...[more]

PMID: 29029016

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Project description:ALS Compute

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