Code associated with Muncie-Vasic et al. bioRxiv 2024 manuscript (https://doi.org/10.1101/2024.11.01.621613)
Full documentation and tutorials for each of the main software packages used can be found from their developers:
- Seurat: https://satijalab.org/seurat/
- ArchR: https://www.archrproject.com/index.html
- MIRA: https://mira-multiome.readthedocs.io/en/latest/index.html
- CellOracle: https://morris-lab.github.io/CellOracle.documentation/
Subdirectories for "Seurat_Analyses" and "ArchR_Analyses" contain scripts for inital analyses (numbed "1_", "2_", etc.), as well as scripts specific to generating figure plots. The scripts for generating figure plots require that all inital analyses scripts have been completed.