Tools

Tumour microenvironment R

CellTFusion

Integrates immune cell-type deconvolution with prior-knowledge TF–gene networks to characterise cell states of the tumour microenvironment from bulk RNA-seq.

GitHub Documentation Paper

Cell-type deconvolution R

multideconv

Integrative pipeline for cell-type deconvolution from bulk RNA-seq, combining first- and second-generation methods.

GitHub Documentation Paper

Cell-type deconvolution R

multimethconv

Integrative pipeline for cell-type deconvolution from DNA methylation data.

GitHub Documentation

Cell–cell communication R

RaCInG 2.0

Random graph model to infer cell–cell communication networks in the tumour microenvironment from bulk RNA-seq.

GitHub Documentation

Machine learning R

pipeML

Modular machine-learning framework for leakage-free classification and survival models through custom cross-validation fold construction.

GitHub Documentation Paper

Spatial networks Python

tysserand

Fast and accurate reconstruction of spatial networks from bioimages.

GitHub Paper

Spatial networks Python

MOSNA

Multi-omics spatial network analysis — patterns and community detection in spatial networks.

GitHub Paper

Spatial networks Rust

MOSNA GUI

Graphical interface for tysserand and MOSNA to build spatial cell networks, compute assortativity and run niche analysis without coding.

GitHub

Genome architecture TypeScript

GARDEN-NET

Genome ARchitecture DNA Epigenome and Nucleome — Network Exploration Tool for 3D chromatin interaction networks.

GitHub Documentation Paper

Agent-based modelling Python

PhysiGym

Bridges the Gymnasium reinforcement-learning interface and the PhysiCell agent-based modelling software.

GitHub Paper

AI agents Python

mcp-tme-servers

A collection of MCP servers that let AI agents study the tumour microenvironment from bulk RNA-seq data.

GitHub