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How to run on end to end script:
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Edit config.yaml (/scripts/input/config.yaml)
- Path to cbioportal data
- Path to list of gene sets to use
- Path to output file
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Run!
- 'cd scripts'
- 'python getGSEA.py {path to sample list}'
- By default, the program will use all samples in the data file. Provide a list of samples to select samples within the data file.
How to run gsea.ipynb notebook:
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Edit dataFile, geneSetFile, resultFile
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Run 'Run GSEA'
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Run 'plotGSEA({Gene Set Term})' for GSEA enrichment plot for one gene set
How to run visualize.ipynb notebook:
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First run gsea.ipynb or the end to end script
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Run the script (: