PADOG is a standard Bioconductor style R package that can be used to perform gene set analysis (e.g. pathway analysis) using microarray data. It differs from other existing approaches mainly by down-weighting the genes that appear in more than one gene sets at the same time.
The package can be downloaded from the Biconductor here.
The method is described in detail in the reference below:
- Tarca AL., Draghici S., Bhatti G., Romero R., Down-weighting overlapping genes improves pathway analysis, BMC Bioinformatics, 2012, 13:136.