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 sctkIf you encounter dependency clashes, create a fresh python 3.9 virtual environment (e.g. via conda) and install SCTK there. It may also help to update pip:
pip install --upgrade pipSCTK's documentation is available here, and features a tutorial and API reference for scAutoQC (an automated QC workflow).
