Single Cell analysis Tool Kit: A large collection of functions built around the scanpy ecosystem that faciliates preprocessing, clustering, annotation, integration and some down-stream analysis of scRNA-seq data.
pip install git+https://github.com/Teichlab/sctk.gitIt is recommended to install sctk into a fresh python 3.9 virtual environment due to its large amount of dependencies. If you encounter a dependency conflict when installing into a fresh environment, try updating pip:
pip install --upgrade pipAn example of applying the automatic QC workflow can be found in the demo notebook.