.. Cellsnake Documentation
   :author: Sinan U. Umu
   :copyright: Copyright (c) 2023, University of Oslo.
   :date: 2023

.. image:: cellsnake-logo-blue-small.png
   :scale: 60 %
   :align: center
   :alt: Cellsnake logo

Welcome to **Cellsnake**'s Documentation!
-----------------------------------------

**Cellsnake** is a command line tool designed for easy and scalable single-cell analysis. It can be used as a Snakemake workflow or as a standalone command line tool.

It is build on **Seurat4** but **Seurat5** version is coming soon!

Our main repository location: https://github.com/sinanugur/cellsnake  

Our Snakemake workflow location: https://github.com/sinanugur/scrna-workflow  



.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   installation.rst
   quickstart.rst
   fetalbrain.rst
   fetalliver.rst
   kraken.rst
   markers.rst
   configs.rst
   options.rst
   downstream.rst
   glossary.rst