Metadata-Version: 2.3
Name: sctk
Version: 0.2.3
Summary: single cell analysis tool kit based on scanpy
License: GPL-3.0
Author: nh3
Author-email: nh3@users.noreply.github.com
Requires-Python: >=3.9,<4.0
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Dist: adjustText (>=0.8,<0.9)
Requires-Dist: harmonypy (>=0.0.9,<0.0.10)
Requires-Dist: leidenalg (>=0.10.0,<0.11.0)
Requires-Dist: numpy-groupies (>=0.9.22,<0.10.0)
Requires-Dist: scanpy (>=1.9.3,<2.0.0)
Project-URL: Documentation, https://teichlab.github.io/sctk/
Project-URL: Homepage, https://github.com/Teichlab/sctk
Description-Content-Type: text/markdown

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# sctk

**S**ingle **C**ell analysis **T**ool **K**it: 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

```bash
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:

```bash
pip install --upgrade pip
```

## Usage and Documentation

SCTK's documentation is available [here](https://teichlab.github.io/sctk/), and features a tutorial and API reference for scAutoQC (an automated QC workflow).

<img src="docs/notebooks/scautoqc_logo.png" alt="scautoqc_logo" width="200"/>
