The main figures of the paper Space-time logic of liver gene expression at sublobular scale can be recreated from this code. All the computations are done in the script "Analysis.ipynb".
These instructions will get you a copy of the project up and running on your local machine for reproducibility purposes.
We recommend you use Anaconda as a Python distribution in order to meet the required most of the Python packages used in this project. The following Python packages are used in the code:
- numpy
- matplotlib
- copy
- pandas
- warnings
- seaborn
- scipy
- signal
- multiprocessing
- operator
- xlsxwriter
- os
- statsmodels
- plotly
The script is a Jupyter Notebook using Python 3.7. After installing Jupyter (e.g. with Anaconda), simply run "jupyter notebook" with a terminal running in the repository and select the notebook.
Supplementary analysis (e.g. David analysis, smFISH) are available upon request.
The code may not be up to PEP8 standards as it was intially not supposed to be shared. However, we decided to make it publicly available to keep our research as transparent as possible. We will update this code with a cleaner version as soon as possible. In the meanwhile, if anything is unclear, do not hesitate to contact the authors (cf. below).
In case of question about the code, please contact colas.droin [at] epfl.ch and jakob.elkholtei [at] unibas.ch. In case of question about the study, please contact felix.naef [at] epfl.ch