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Netpredictor - An R package for network analysis and prediction
  • Abhik Seal,
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Abstract

Netpredictor is an R package for prediction of missing links in any given bipartite network. The package provides utilities to compute missing links in a bipartite and well as unipartite networks using Random Walk with Restart and Network inference algorithm.  The package also allows computation of Bipartite network properties, visualization of communities for two different sets of nodes, and calculation of significant interactions between two sets of nodes using permutation based testing. Analysis of PPI network like finding shortest paths in a network and extraction of subgraphs from PPI data functionality is currently available for Consensus path and String database.   The tool also have an enrichment analysis option for performing  enrichment of diseases based on disgenet, pathways (reactome) and gene-ontology. The R standalone package (including detailed introductory vignettes) and associated R Shiny web application is available under the GPL-2 Open Source license and is freely available to download from Netpredictor and Shiny Netpredictor repository respectively.