Python implementation of the Gene Set Enrichment Analysis method
Above the directory containing setup.py, install using: >>pip install -e gsea
This software has been tested in an Anaconda environment containing the following packages and their respective dependencies:
- python (v. 3.6.1)
- numpy (v. 1.12.1)
Currently, the package can be run from the root directory as follows:
>> python gsea <filename1> <filename2>
where filename1 refers to the Gene Expression Profile data, and filename2 refers to the Gene Set data. The gsea/config.py file determines the location of the data (must be in the python path), the output filename, as well as several analysis parameters.
config.py is meant to be easily edited by the user.
The default filename for outputting the results is "results.csv". The default directory for input and output file locations is "data."