CRC Immune Hub expression program analysis

Principal analysis code used in "Spatially organized multicellular immune hubs in human colorectal cancer".

Installation

Clone the repository from github:

git clone https://github.com/matanhofree/crc-immune-hubs.git

Prerequisites:

Matlab (>R2019a)
python (3.7) & jupyter

Data download

Data from used in the analysis can be downloaded from the supplemental website to a data folder.

For example you can use wget:

wget -r -np -nH --cut-dirs=2 -R "index.html*" https://portals.broadinstitute.org/crc-immune-hubs/extra/data/colon10x_default/
wget -r -np -nH --cut-dirs=2 -R "index.html*" -R "*.tar.gz" https://portals.broadinstitute.org/crc-immune-hubs/extra/data/matlab/
wget -r -np -nH --cut-dirs=2 -R "index.html*" https://portals.broadinstitute.org/crc-immune-hubs/extra/data/cNMF_tSNE/

Jupyter notebooks

The notebooks folder of this repo contains jupyter notebooks for reproducing the key figures included in our publication.
These notebooks use the Calysto/matlab_kernel to remotely run matlab code in jupyter notebooks instance. See the following for instructions on how to configure this jupyter_kernel: [1], [2].

Under construction