README.md

Apply phenotypic profiling model to JUMP data

In this module, we generate single-cell probabilities for each of the 15 phenotypic classes by applying the phenotypic profiling model. There are two model types, final and shuffled baseline. The shuffled baseline model trains using randomly shuffled single-cell features. We output one file for all plates that contains phenotypic probabilities and relevant metadata for all of the single-cells. The files we output are in parquet format.

Run the prediction notebook

To generate the probabilities for each single cell, run the evaluate_data.sh file which will convert the notebook into a python file and run it from terminal.

# Make sure you are in the 2.evaluate_data directory
cd 2.evaluate_data
# Run the notebook as a python script
source evaluate_data.sh