.. RECODE documentation master file, created by
   sphinx-quickstart on Fri Oct  8 15:45:48 2021.
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RECODE documentation
====================================
**Re**\ solution of the **c**\ urse **o**\ f **d**\ im\ **e**\ nsionality (RECODE) is a noise reduction method for single-cell sequencing data. `github <https://github.com/yusuke-imoto-lab/RECODE>`_

.. image:: ../../images/RECODE_procedure.jpg

`Y. Imoto, T. Nakamura, et al. Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis, 2022, Life Science Alliance <https://dx.doi.org/10.26508/lsa.202201591>`_.

`Y. Imoto. Comprehensive Noise Reduction in Single-Cell Data with the RECODE Platform, 2024, bioRxiv <https://doi.org/10.1101/2024.04.18.590054>`_.

The license gives permission for personal, academic, or educational use. 
Any commercial use is strictly prohibited. 
Please contact imoto.yusuke.4e\<at\>kyoto-u.ac.jp for licensing terms for any commercial use.


Installation
====================================
The python package of RECODE supports PyPI install. 

.. code-block:: bash

 $ pip install screcode


You can also install the development version of lingam package from GitHub:

.. code-block:: bash

	$ pip install git+https://github.com/yusuke-imoto-lab/RECODE.git

If the installation fails, try installing again by appending `#subdirectory=python` or `\#subdirectory=python` at the end.

To use RECODE, import ``screcode``. 

.. code-block:: python

 import screcode


The R package is available `here <https://github.com/yusuke-imoto-lab/RECODE/tree/main/R>`_.

.. toctree::
	:maxdepth: 2
	:caption: Contents:
	
	Tutorials/index
	reference/index


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

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