Pathway-PDM is a method for identifying differentially regulated pathways. Pathway-PDM is nonparametric and completely data-driven (no user-set parameters). Importantly, Pathway-PDM is able to detect altered pathways even when the individual genes are not...
How do we know that a network analysis method works? Testing against synthetic data (where the truth is known by construction) is a common approach, but lacks the statistical idiosyncrasies of experimental data. An alternative approach is to test whether the method...
PoDA is a pathway-based, multi-SNP analysis method for GWAS data based upon the hypothesis that if a pathway is related to disease risk, cases will appear more similar to other cases than to controls for the SNPs associated with that pathway. PoDA improves on existing...
GeneSurrounder is a new network-based analysis method for transcriptomic data that identifies sources of disregulation. It achieves this by quantifying patterns of differential expression on the network surrounding each gene, and returns a ranked list of putative...
