single cell analysis tool kit based on scanpy
Project description
sctk
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.
Installation
pip install sctk
If 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 pip
Usage and Documentation
SCTK's documentation is available here, and features a tutorial and API reference for scAutoQC (an automated QC workflow).
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