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Running on SGA data

  1. Follow the instructions in the readme file for installing (takes a while).
  2. Activate the virtual environment by running poetry shell.
  3. To make sure that it works, and to download the necessary files:
    1. Remove the content of the folder results
    2. Run bash get_data.sh; bash example_enrichment.sh (this should generate two files in the folder results/).
  4. Copy the file SGA_aal1D_aal1OE_Any_Two_overlap_and_Background.xlsx into the folder data. This file should be an excel file with the following columns:
    1. aal1D_Any_Two_Overlapped
    2. aal1D_Background
    3. aal1OE_Any_Two_Overlapped
    4. aal1OE_Background
  5. Then run bash enrichment_shajahan.sh (see comments in the script). That should write the output files in the results/ directory.