NetRep | R package containing functions

NetRep is a R library. NetRep has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

An R package containing functions for assessing the replication and preservation of a network module's topology across datasets through permutation testing. This is suitable for networks that can be meaningfully inferred from multiple datasets. These include gene coexpression networks, protein-protein interaction networks, and microbial interaction networks. Modules within these networks consist of groups of nodes that are particularly interesting: for example a group of tightly connected genes associated with a disease, groups of genes annotated with the same term in the Gene Ontology database, or groups of interacting microbial species, i.e. communities. Application of this method can answer questions such as; (1) do the relationships between genes in a module replicate in an independent cohort? (2) are these gene coexpression modules preserved across tissues or tissue specific? (3) are these modules conserved across species? (4) are microbial communities preseved across multiple spatial locations?. The main function for this package is modulePreservation, which performs the permutation test procedure. Other useful functions include networkProperties for calculating the topological properties of a module, and plotModule for visualising a network module. For more information see the associated publication in Cell Systems, A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.