R package for the identification of functionally important subnetworks
Crosstalkr is an extension of the crosstalker webapp developed by Neoproteomics and Case Western Reserve University School of Medicine. It is a free, open-source R package designed to provide the same functionality as the crosstalker webapp in a modular fashion that can be incorporated into existing bioinformatic pipelines.
Given a set of user-provided set of seed proteins, crosstalkr will identify enriched subnetworks of genes that have a high affinity for the provided seeds. This is accomplished using random walks with restarts, starting at the user-provided seed proteins. Random walks are implemented using sparse matrix multiplication to facilitate fast execution.
Affinity scores from a given random walk with restarts are compared to a bootstrapped null distribution to assess statistical significance. More detailed methodology can be found here: "Nibbe et al., An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer, Comput Biol 6(1): e1000639. doi:10.1371/journal.pcbi.1000639"
Please feel free to submit issues here. You can also contact me at davis.weaver@case.edu if you have any questions.