Network-Based Gene Set Analysis

Description

The netgsa-package provides functions for carrying out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.

Details

Author(s)

Ali Shojaie <ashojaie@uw.edu> and Jing Ma <mjing@umich.edu>

References

Ma, J., Shojaie, A. & Michailidis, G. (2014). Network-based pathway enrichment analysis with incomplete network information, submitted. http://arxiv.org/abs/1411.7919.

Shojaie, A., & Michailidis, G. (2010a). Penalized likelihood methods for estimation of sparse high-dimensional directed acyclic graphs. Biometrika 97(3), 519-538. http://biomet.oxfordjournals.org/content/97/3/519.short

Shojaie, A., & Michailidis, G. (2010b). Network enrichment analysis in complex experiments. Statistical applications in genetics and molecular biology, 9(1), Article 22. http://www.ncbi.nlm.nih.gov/pubmed/20597848.

Shojaie, A., & Michailidis, G. (2009). Analysis of gene sets based on the underlying regulatory network. Journal of Computational Biology, 16(3), 407-426. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131840/

See Also

glasso, glmnet

Results