Analysis repository regarding review comments for:
"Cell-intrinsic Aryl Hydrocarbon Receptor signalling is required for the resolution of injury-induced colonic stem cells"
- Linux/Unix platform (macOS supported)
- Conda installed
Clone this repository, navigate to the folder using the command line and install the conda environment using
conda env create -f environment.yml
To generate the bed files which are consumed by the downstream analysis, run generate_beds.sh
To view the downstream analysis just click on analysis.ipynb in the browser on github.
To re-run the analysis, start jupyter by typing jupyter lab from the root repository folder, then open either analysis or ucsc_export and re-run the steps.
This script will format and normalise the data for display in UCSC browser. All bed files can be directory uploaded from _ucsc_export to the browser as custom tracks.
This script contains all the steps to generate the figures and stats used in answering the relevant reviewer questions.