/hackhigh

cBioPortal Hackathon

Primary LanguageJupyter Notebook

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Hackhigh - GSEA analysis from cbioportal mRNA samples

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How to run on end to end script:

  1. Edit config.yaml (/scripts/input/config.yaml)

    • Path to cbioportal data
    • Path to list of gene sets to use
    • Path to output file

  2. 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:

  1. Edit dataFile, geneSetFile, resultFile

  2. Run 'Run GSEA'

  3. Run 'plotGSEA({Gene Set Term})' for GSEA enrichment plot for one gene set

How to run visualize.ipynb notebook:

  1. First run gsea.ipynb or the end to end script

  2. Run the script (: