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

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

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

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

Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis

Spatial analysis toolkit for single cell multiplexed tissue data

Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data

Infer cell-cell communications based on feed-forward neural network

Differential communication analysis for scRNAseq datasets based on expression products

SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

A study of the crosstalk between cancer cells and tumor microenvironmental cells.

Project on ABM tumor growth for the Agent-Based Modeling course at the UvA 2023-2024

Goo is the Blender library for simulating biological cells, tissues and embryos in 3D.

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

Spatially Resolved Chimeric Analysis

Multi-level Graph Autoencoder (GAE) to clarify cell cell interactions and gene regulatory network inference from spatially resolved transcriptomics