2025/01/01 by David Kainer, Matthew Lane, Kyle A. Sullivan +20 · 2 voices
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Gene Regulatory Network Analysis #Gene expression and cancer classification
paper · pdf · doi:10.1093/gigascience/giaf028
openalex publication_date 2025/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/03
We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.