.. scAE-batch documentation master file, created by
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Welcome to cyclum's documentation!
==================================

Cyclum is a package to tackle cell cycle.
It provides methods to recover cell cycle information and remove cell cycle factor from the scRNA-seq data.
The methodology is to rely on the circular manifold, instead of the marker genes.
Multiple methods suits this idea.
We provide an Auto-Encoder based realization at this time, and we are adding Gaussian Process Latent Variable Model soon.
Also provided are a set of supplementary tools to visualize and anaylzing the result, in python and in R.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   download_install
   usage
   quick_start
   input_formats
   output_formats
   customization
   modules
   faq
   features
   license

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`