The subnetwork toolkit is a set of tools to analyze gene sub-networks:
- Background: creates background gene network.
- Gene-level SAM: runs
SAM R module in the gene-level.
- Search: given a background network and a certain property, searches sub-networks that maximize the property.
- Clustering: clusters list of subnetworks using hierarchical clustering
- Enrichment Test: executes gene set enrichment for sub-networks.
- Convert: converts Entrez gene ids to gene symbols in a gene set file or vice versa.
- Export: exports sub-networks with GraphML file format.
- Filter: filter sub-networks.
- Sub-network GSA: runs the gene set analysis (GSA).