Ludwig-ISPY2

Paper

• https://www.cell.com/cancer-cell/fulltext/S1535-6108(22)00216-1

Steps for running a Ludwig experiment:

1. Download and prepare the data: make download-and-prepare-data This will create two files, ispy2_phenotype.tsv and ispy2_expression_std_sorted.tsv
2. Run Ludwig experiment: make ludwig-experiment. This will (1) create the needed configuration file for Ludwig; (2) prepare the data for the experiment by scaling it and combining the X and Y matrices; (3) run Ludwig on the prepared data using the configuration file.