CePa is a useful tool to find significant pathways from pathway structure information. The motivation of the software is that the traditional over-representation analysis (ORA) methods find significant pathways without the topological information. The tool also emphasizes that multiple choices to look for important nodes in network is necessary.
- R package
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CePa: an R package for finding significant pathways weighted by multiple network centralities.
Gu Z, Wang J.
Bioinformatics. 2013 Mar 1;29(5):658-60. doi: 10.1093/bioinformatics/btt008. Epub 2013 Jan 10.