bio2bel-msig 0.0.3

Installation

This code can be installed with pip3 install git+https://github.com/bio2bel/msig.git

The package expects you have downloaded the gene sets from MSigDB following the instructions and terms stated in their website. The gene sets in gmt format should placed in /resources. However, feel free to change the directory by modifying the constants module.

Functionalities and Commands

Following, the main functionalities and commands to work with this package:

• Populate local database with MSigDB python3 -m bio2bel_msig populate --path='/my/path/to/genesets/msigdb.v6.1.symbols.gmt'

• Run an admin site for simple querying and exploration python3 -m bio2bel_msig web (http://localhost:5000/admin/)

• Export gene sets for programmatic use python3 -m bio2bel_msig export

Citation

• Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., … & Mesirov, J. P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550.

• Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.