Emergent statistical laws in single-cell transcriptomic data

Code to reproduce the statistical data analysis of Mouse Cell Atlas and Tabula Muris compendium proposed in the paper "Emergent statistical laws in single-cell transcriptomic data".

Analyses

Tabula Muris

It contains a notebook where is available the code used to analyze the Tabula Muris transcriptomic data. Tabula_Muris_Data_Analysis.ipynb

Mouse Cell Atlas

In this folder it is possible to reproduce all the analyses involving Mouse Cell Atlas dataset.

Moreover running combined_analyses.ipynb it is possible to reproduce some analyses comparing different datasets as discussed in the paper.

Additional Tools

Download the data

Part of the data and results in this repository are stored using Data Version Control dvc tool.

It is possible to retrieve the data running

dvc pull -r mydrive

Run in a Docker container

It is possible to run all the notebooks in this repository in a controlled container simply running

cd docker
docker-compose up -d

and then pointing a browser to localhost

Paper

S. Lazzardi, F. Valle, A. Mazzolini, A. Scialdone, M. Caselle and M. Osella, Emergent statistical laws in single-cell transcriptomic data, Physical Review E (2023)

License

See LICENSE