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COSG: COSine similarity-based marker Gene identification
========================================================

COSG is a cosine similarity-based method for more accurate and scalable marker gene identification.

- COSG is a general method for cell marker gene identification across different data modalities, e.g., scRNA-seq, scATAC-seq and spatially resolved transcriptome data.
- Marker genes or genomic regions identified by COSG are more indicative and with greater cell-type specificity.
- COSG is ultrafast for large-scale datasets, and is capable of identifying marker genes for one million cells in less than two minutes.

The method and benchmarking results are described in `Dai et al., (2022) <./references.html>`_. Additionally, the R version of COSG is available `here <https://github.com/genecell/COSGR>`_.

Note: we have recently released our python toolkit, `PIASO <https://github.com/genecell/PIASO>`_, in which some methods were built upon COSG, please try out PIASO, thank you!

.. toctree::
   :maxdepth: 1

   installation
   tutorials
   modules
   references
   releaseNotes


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

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