README.md

ggo-imc

This repository contains the code to reproduce figures from manuscript: "Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression."

Data

The processed data and raw data (for further exploration) can be found at Zenodo (view of the data might be restricted until publication):

• - Processed Data
• - Raw Data

Environment Setup

# setting up conda environment
conda create -n ggo-imc python==3.9 -y
conda activate ggo-imc
pip install -r requirements.txt

Analysis Pipeline

For streamlined analysis to produce figures use the command

make run

Alternatively for individual plots for each figures:

make figure1
make figure2
make figure3
make figure4
make figure5