This repository contains the code for the analysis presented in the paper:
Mynster Kronborg, T., Webel, H., O’Connell, M. B., Danielsen, K. V., Hobolth, L., Møller, S., Jensen, R. T., Bendtsen, F., Hansen, T., Rasmussen, S., Juel, H. B., & Kimer, N. (2023).
Markers of inflammation predict survival in newly diagnosed cirrhosis: a prospective registry study.
Scientific Reports, 13(1), 1–11.
https://www.nature.com/articles/s41598-023-47384-2
The core functionaly used is available through the python package njab, which can be installed from PyPI: pypi.org/project/njab
The Snakemake workflow builds the data and analyis from the raw data. It was executed locally. It allowed to easily re-run the entire pipeline if the data was updated during the course of the study or if the analysis was updated.
cd analysis
snakemake -n
Please see the analysis README for more details.
The data is unfortunately not available for download. The repository is meant for documenting the analysis steps and local execution.
The environment was build using conda
# in repo directory
conda env create -f environment.yml
conda activate cirrhosis_death
In case you want to inspect the packages in a concrete environment, we provided a dump in environment_231109_win64.yml.