sctk 0.2.2

single cell analysis tool kit based on scanpy

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).