netgsa-package: Network-Based Gene Set Analysis

In netgsa: Network-Based Gene Set Analysis

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 <[e-mail]>, Jing Ma, Michael Hellstern <[e-mail]>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. \Sexpr[results=rd]{tools:::Rd_expr_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/

See Also

glmnet

netgsa documentation built on Nov. 14, 2023, 5:09 p.m.