Tools

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

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

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

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

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

Fast and accurate reconstruction of spatial networks from bioimages.

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

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

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

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