R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

NicheNet: predict active ligand-target links between interacting cells

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

LIANA: a LIgand-receptor ANalysis frAmework

LIANA+: an all-in-one framework for cell-cell communication

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Learning cell communication from spatial graphs of cells

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

R package to do the Ligand Receptor Analysis Visualization

Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

Source code for Liu, Y., Li, J. S. S., Rodiger, J., Comjean, A., Attrill, H., Antonazzo, G., ... & Perrimon, N. (2022). FlyPhoneDB: an integrated web-based resource for cell–cell communication prediction in Drosophila. Genetics, 220(3), iyab235.

SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics

A manually curated database of literature-supported ligand-receptor interactions in human and mouse

Spatial direct messaging detected by bivariate Moran

HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes

LIANA x Tensor-cell2cell Protocols