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