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.
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.¶
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