This package enables condition- and cell-type-specific analysis of transcription factor activities and generates intracellular signaling Networks. The results can be combined with ligand-receptor predictions and analyzed differentially using CrossTalkeR.
To perform receptor perturbation simulation, use the Python package IntraTalkerpy
Single-cell sequencing has advanced the study of cell-cell communication, yet most methods focus on intercellular ligand- receptor interactions while neglecting downstream intracellular signalling cascades and the possibility that downstream target genes themselves encode ligands, thereby propagating communication across multiple cells. We present In- traTalker+CrossTalkeR that combines intracellular (IntraTalker) and intercellular (CrossTalkeR) signalling from multimodal single-cell data. IntraTalker infers cell-type-specific transcription factor activities and constructs receptomes that link receptors to downstream target genes, which are then integrated with ligand-receptor predictions in CrossTalkeR. To prioritize signalling receptors, the framework performs in silico receptor perturbation.
Install the package from GitHub with devtools:
# Install devtools if necessary
install.packages("devtools")
# Install the package
devtools::install_github("CostaLab/IntraTalker")or with the remotes package:
# Install remotes if necessary
install.packages("remotes")
# Install the package
remotes::install_github("CostaLab/IntraTalker")