Written for [NYU Master in Biomedical Informatics - Intro to Python] Final Project
By:
- Jeff Zhang
- Helena Jun
- Divya Mandalaywala
- Zhang Yu
The Github repository aims to replicate R processing of data in the following paper with Scanpy: https://link.springer.com/content/pdf/10.1007/s11684-020-0754-0.pdf
The functions aim to provide a way a reuseable way to process and visualize scRNA data using Scanpy according to the requirements and parameters of the user.
- "main_complete.ipyb" provides a notebook file for sequential code
- "main_python.py" provides a python file of "main_complete.ipynb"
Packages used can be found on "requirements.txt" and can be loaded via pip
To Run Program Examples:
- Install packages with "pip install -r requirements.txt"
- Run all cells in main_complete.ipynb