MATLAB implementation of Gene Set Enrichment Analysis (GSEA) method for finding pathways which can show more complex relation between changes of gene expression due to different phenotypes. Major adjustments of the method:
- 12 gene ranking metrics implemented (plus its ranks and/or absolute values)
- possibility to use external ranking metric method (by applying own function)
- possibility to use external Gene Set Database
- phenotype permutation available for all ranking methods (even external ranking)
- increased efficiency by parallel computing used
if you use this software please cite:
Zyla, J., Marczyk, M., Weiner, J., & Polanska, J. (2017). Ranking metrics in gene set enrichment analysis: do they matter?. BMC Bioinformatics, 18(1), 256
Author: Michał Marczyk and Joanna Żyła