Flexible Gene Set Enrichment Analysis

flexgsea is a R package to do gene set enrichment analysis [1]. Main advantages:

• Allows user defined functions. So you can use you favorite package for differential expression.
• Calculates significance by sample permutation.
• Parallelization using the foreach package.
• Can calculate normalized enrichment scores (NES) and significance based on that.
• Implements the weighted KS-like statistic.

The package is not yet on CRAN. You can install from Github:

# install.packages("devtools")
devtools::install_github("NKI-CCB/flexgsea-r")

Main documentation is on the flexgsea function in the package:

help('flexgsea', 'flexgsea')

This package was called ggsea before.

References

[1] Subramanian, Aravind, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, et al. 2005. "Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles." Proceedings of the National Academy of Sciences of the United States of America 102 (43): 15545–50. doi:10.1073/pnas.0506580102.