Known Issues

Windows OS has known issues with Scanpy and thus generates a higher number of clusters with a given Leiden resolution value. A numpy conflict may provide a value error message, ignore the warning. For optimal performance, consider using WSL to download the CAFE folder from Github using git clone and run the app using Pixi.

git clone https://github.com/mhbsiam/cafe.git

Here is a tutorial on how to install and activate WSL on a Windows computer. Finally, while reporting data generated using CAFE, mentioning the operating system used for data generation is highly recommended for replicability.