Scripts for CISI-IMC publication
ipynb files to perform analyses demonstrated in the manuscript. First line of each file indicates which figure it corresponds to.
python files contaning functions used in the codes in "analysis" folder.
- simulate_A: Simulating the decompression performance of barcoding matrix.
- smaf: Calculating dictionary from single cell expresssion data.
- utils: other functions
Demo ipynb script to go through CISI-IMC workflow with a subset of our datasets. Simply run Demo_cisi_imc.ipynb. Data needed to run the demo script is stored in demo/data/ folder.
yml file to create a python environment for CISI-IMC. This may take a few minutes.
conda env create -f env/cisi_imc_env.yml
conda activate cisi_imc_envRmd files to produce the plots in the manuscript.