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

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

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

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

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

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

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

Spatial direct messaging detected by bivariate Moran

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

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

Identifying external communication signals using single-cell transcriptomics data

ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods