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IntraTalkerPy documentation
===========================

IntraTalkerPy combines transcription factor analysis and gene expression perturbation analysis for single-cell data.

The transcription factor module estimates transcription factor activities using decoupleR. Using the DoRothEA regulon version from decoupleR and post-translational interactions from the Omnipath database[2,3,4], connections are made between transcription factors and ligands and receptors.

The results can be combined with ligand-receptor interactions and then analyzed using CrossTalkeR (https://github.com/CostaLab/CrossTalkeR/) [5].

The original R version can be found here: (https://github.com/CostaLab/IntraTalker/)

The perturbation module provides methods, utilities, and plotting functions for receptor-related gene expression perturbation workflows.

.. figure:: _static/Workflow_Overview_BG.png
   :alt: IntraTalker + CrossTalkeR workflow: cell-type-specific TF activities and receptomes from scRNA-seq and scATAC-seq, integrated with ligand-receptor predictions in CrossTalkeR 2.0, followed by in silico receptor perturbation
   :align: center
   :width: 100%

   From scRNA-seq and scATAC-seq to prioritized receptors: IntraTalker infers
   transcription factor activities and receptomes, CrossTalkeR 2.0 integrates them with
   ligand-receptor predictions, and the perturbation module ranks receptors by their
   simulated knockout effect.

.. toctree::
   :maxdepth: 3
   :caption: Contents:
   
   install
   support
   tutorials/index
   api