1. cMonkey2

    • cMonkey2 source code - Clone the latest release of cMonkey2 from GitHub.

    • Example cMonkey2 run - When expanded and all dependencies of running cMonkey2 are met this will run with 2,000 genes (full runs in paper have 9,138 genes). Requires that paths to cMonkey2 be set properly. We added symbolic links to the config and cmviewer directories into the gbm.cMonkey2 directory and were able to run to completion.
      • Currently configured to run with PITA set-enrichment (miRNA). To reconfigure for TargetScan (miRNA) or TF-target gene databaset (TF) simply change the gbmTCGA.ini file to point at the appropriate JSON file.

  2. TF-target gene database

    • TF-target gene database - We provide the TF target gene predictions as separate CSV files for each TF motif. We also provide a conversion file that maps motif names to their cognate TF.

  3. SYGNAL pipeline

    • SYGNAL pipeline source code - The SYGNAL pipeline is designed to be cloned into a completed cMonkey2 run directory. It will then run the SYGNAL pipeline using the cMonkey2 result database and put all the results into 'sygnal/output' directory, which it will create if not already present. There is fairly through checkpointing as the full SYGNAL pipeline can take some time to run.

    • Example SYGNAL pipeline run - When expanded and placed inside a completed cMonkey2 (works in example run above). Need to meet all dependencies of running SYGNAL pipeline.