Changes in blood cell deformability in Chorea-Acanthocytosis and effects of treatment with dasatinib or lithium

This repository contains data files and analysis tools to recreate the plots for Reichel et al. 2021. "Changes in blood cell deformability in Chorea-Acanthocytosis and effects of treatment with dasatinib or lithium", https://www.biorxiv.org/content/10.1101/2021.12.16.472921

The folder figure_plots contains Jupyter notebooks that were used to create the figures.

To run the notebooks an installation of python>=3.7 is needed.

The requirements.txt and environment.yml contain all dependencies for the notebooks to work and can be installed either with pip or conda. Please create an virtual environment, e.g. with Anaconda's conda create command and run the following commands:

Create a conda virtual environment from the environment.yml by running:

conda env create -f environment.yml

The default environment name will be py37_chac

Or from the requirements.txt:

# using Conda
conda create --name <env_name> --file requirements.txt

# using pip
pip install -r requirements.txt

For significance testing, a valid installation of R>3.0 is needed and one needs to install the lme4 package from CRAN (R -e "install.packages('lme4', repos='http://cran.r-project.org')"). But the analysis is also run through the Jupyter notebooks.

The folder data_preparation contains notebooks that describe how the raw data was processed to get the data that is used to create the figure plots (data under figure_plots\data). The raw data is available on figshare: https://doi.org/10.6084/m9.figshare.c.5793482 .