Identification of Parkinson’s disease-associated regulatory variants in human dopaminergic neurons reveals modulators of SCARB2 and BAG3 expression

Please cite the following reference:

All the scripts have been run into a Docker container based on r2u.
This repository contains the code and data to reproduce the figures of the manuscript. Every figure has its own folder with the related data to it.

Docker container

• To build the image from the folder containing the Dockerfile: docker buildx build -t 250603:24.04 .

Of note, ensure that renv is not invoked if you use it: mv .Rprofile Rprofile

• To start a container from the image, binding the local directory: docker run -u $(id -u):$(id -g) -ti -v pwd:/mnt 250603:24.04

Once in the container, for Figure3 for example: cd /mnt/FIGURE3 ; Rscript --vanilla Figure3.R

Data availability

Sequencing of epigenetics data can be found at EGA-archive under controlled access.

Acknowledgements

• The sequencing was performed at the Genomics Platform of Luxembourg Centre for System Biomedicine.
• The computational analysis presented in this paper were carried out using the HPC facilities of the University of Luxembourg https://hpc.uni.lu.
• Figures created with the plotgardener R package.
• Figure 1A was created with BioRender using license Catillon, M. (2025) https://BioRender.com/5kzs36o.

References

• R Core Team (2025). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org.
• Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). "Welcome to the tidyverse." Journal of Open Source Software, 4(43), 1686. doi:10.21105/joss.01686 https://doi.org/10.21105/joss.01686.
• Nicole E Kramer, Eric S Davis, Craig D Wenger, Erika M Deoudes, Sarah M Parker, Michael I Love, Douglas H Phanstiel, Plotgardener: cultivating precise multi-panel figures in R, Bioinformatics, 2022.
• Jesper R Gådin, Ferdinand van't Hooft, Per Eriksson and Lasse Folkersen (2015): AllelicImbalance: an R/bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing. BMC Bioinformatics.
• Kassambara A (2025). ggpubr: 'ggplot2' Based Publication Ready Plots. R package version 0.6.2, https://rpkgs.datanovia.com/ggpubr.