Welcome to CellBender's documentation!
======================================

.. image:: /_static/design/logo_250_185.png
   :height: 185 px

*CellBender* is a software package for eliminating technical artifacts from high-throughput
single-cell RNA sequencing (scRNA-seq) data.

For a brief survey of the package and its current capabilities, you can read
the :ref:`Introduction <introduction>`.

For an explanation of when and how and why to use CellBender in your analysis
pipeline, along with example code, how to choose parameter settings, and
tips on quality control, read the :ref:`Usage <usage>` section.

For a step-by-step tutorial on a simplified example dataset, see the
:ref:`Quick start tutorial <quick start tutorial>` section.

For details on input arguments and the output file format,
see the :ref:`Reference <reference>` section.

For troubleshooting and an FAQ, see the :ref:`Troubleshooting <troubleshooting>` section.

.. toctree::
   :maxdepth: 1
   
   introduction/index
   installation/index
   usage/index
   tutorial/index
   reference/index
   troubleshooting/index
   contributing/index
   citation/index
   reference/license/index
   changelog/index