Note: This is not the main BANKSY repo. That can be found here: R version, Python version.
The scripts in this repo run with BANKSY version 0.1.5. This is a legacy version that uses a custom BANKSY object (i.e., not the SingleCellExperiment class in the latest version). You can install it using the line: remotes::install_github("prabhakarlab/Banksy@main") # to install 0.1.5.
There are the following major folders in this repository:
- fig3-crc
- fig3-hypothalamus
- fig4-hippocampus
- fig5-dlpfc
- suppfig-codex
- suppfig-cosmx
- artificial-data
The scripts to regenerate the corresponding results are in the src/ folders in these top level directories. The data must be downloaded and placed in the data/ folders, and the instructions to download the data can be found in either the data/README file, or in the beginning of the respective script in the src directory itself.
The SlideSeq and STARmap data analyses can be found in the Jupyter notebooks at the banksy_manuscript branch of the Python repo.