Mirsynergy: detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion.
Mirsynergy is a deterministic overlapping clustering algorithm adapted from a recently developed framework. Mirsynergy operates in two stages that first forms MRM based on co-occurring miRNAs and then expand the MRM by greedily including (excluding) mRNA into (from) the MRM to maximize the synergy score, which is a function of miRNA-mRNA and gene-gene interactions.
The main function
mirsynergy takes as inputs the mRNA and miRNA
interaction matrix and gene-gene interaction matrix provided by the user or
generated from existing techniques described in the manuscript (in preparation).
The function then outputs a list with each item as a miRNA regulatory module
(MRM) containing miRNA and mRNA ID and and other results for diagnostic purpose.
Yue Li Maintainer: Yue Li <email@example.com>
Li, Y. et al. Mirsynergy: detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion. (in preparation).
Nepusz, T., Yu, H., & Paccanaro, A. (2012). Detecting overlapping protein complexes in protein-protein interaction networks. Nature Methods, 9(5), 471-472. doi:10.1038/nmeth.1938
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