Skip to content

Latest commit

 

History

History
15 lines (13 loc) · 604 Bytes

README.md

File metadata and controls

15 lines (13 loc) · 604 Bytes

batch_cell_typing

Analyze the effects of intensity batch correction algorithms on cell typing models (MAPS & XGBoost) for 3 different methods:

  1. COMBAT
  2. MICHEALSON
  3. Z-score normalization

Getting Started

  1. Git pull the MAPS repo + Install related dependencies
  2. Replace the trainer.py script in MAPS/maps/cell_phenotyping/trainer.py with the script in this repo
    • This script only changes the input for the model.fit function to take in dataframes instead of a path
    • Implemented just for ease of use and batch running
  3. Run maps_main.ipynb

TO DO

[] Clean up the ipynb script