| netgsa-package {netgsa} | R Documentation |
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.
Author(s)
Ali Shojaie <ashojaie@uw.edu>, Jing Ma, Michael Hellstern <mikeh1@uw.edu>m and Kun Yue
References
Ma, J., Shojaie, A. & Michailidis, G. (2016) Network-based pathway enrichment analysis with incomplete network information. Bioinformatics 32(20):165–3174. doi:10.1093/bioinformatics/btw410
Shojaie, A., & Michailidis, G. (2010a). Penalized likelihood methods for estimation of sparse high-dimensional directed acyclic graphs. Biometrika 97(3), 519-538. https://academic.oup.com/biomet/article-abstract/97/3/519/243918
Shojaie, A., & Michailidis, G. (2010b). Network enrichment analysis in complex experiments. Statistical applications in genetics and molecular biology, 9(1), Article 22. https://pubmed.ncbi.nlm.nih.gov/20597848/.
Shojaie, A., & Michailidis, G. (2009). Analysis of gene sets based on the underlying regulatory network. Journal of Computational Biology, 16(3), 407-426. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131840/