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Cisformer Documentation
=======================

Cisformer is a Transformer-based framework for cross-modality generation and
regulatory inference in single-cell RNA-seq and single-cell ATAC-seq data. It
supports RNA-to-ATAC prediction, ATAC-to-RNA prediction, and cell-type-specific
cCRE-gene link inference from trained ATAC-to-RNA models.

Version 1.1.0 adds mouse reference support, species-aware config generation,
automatic ATAC-to-RNA log1p detection, and faster link matrix generation.

.. toctree::
   :maxdepth: 1
   :caption: Contents:

   conception.md
   installation.md
   quickstart.md
   usage.md
   publishing.md
   release.md

Index
=====

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