The package contains functions to: - perform network diffusion (ND) on molecular networks; - obtain ND input matrix X0 from gene expression data via kernel estimation; - permute the vertices of a graph, freely, conserving vertex degree and/or conserving disntinct vertex subsets; - normalize adjacency matrix; - normalize ND output matrix Xs; - calculate gene set scores from Xs; - create an enrichment map; - perform over-representation analysis (ORA); - perform gene-set enrichment analysis (GSEA); - plot heatmaps of multiple ORA/GSEA runs; - obtain the functional cartography of a network.
The package provides a gene-level human interactome derived from STRING v12 (https://string-db.org).
Documentation: https://emosca-cnr.github.io/NPATools
Source code: https://github.com/emosca-cnr/NPATools