IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

A collection of tumour microenvironment single-cell RNA sequencing datasets for use in R and other pipelines.

Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2020), including equivalent models using TCGA RNA-seq gene expression and combined microbial abundance and gene expression for comparison.

PhysiGym is a tool for applying reinforcement learning to PhysiCell

Optimized pipelines for Spatial Transcriptomics (ST) data analysis using Seurat & Giotto, designed for reproducible benchmarking and biological insight.

Analysis of treatment naive and neo-adjuvant chemotherapy treated high-grade serous ovarian cancer samples

A classifier for tumor microenvironment subtype based on ensemble machine learning models

A pan-cancer morphology atlas linking histological features to molecular and clinical outcomes

Distinct mesenchymal cell states mediate prostate cancer progression

xCell framework, enabling expert-level tumor microenvironment cell-type enrichment and TME index profiling from bulk transcriptomic data.

Exploratory scRNA-seq analysis of T cell transcriptional states in human lung adenocarcinoma, contextualized within the global tumor microenvironment.

A reproducible framework for modeling spatial cell–cell interactions in the tumor microenvironment using multitype Gibbs point processes and multiplexed imaging data.

SCENIC preprocessing, run & downstream for CRC stroma analysis - Frank et al 2026

LLM-driven multi-agent simulation of the KRAS G12D pancreatic tumor microenvironment — emergent immunosuppression, NK/DC agents, ablation studies. bioRxiv 2026.

This repository contains code and data for the study: "Neoantigens and Stochastic Fluctuations Regulate T Cell Proliferation in Primary and Metastatic M

Single-cell RNA-seq analysis of CD8 T cell functional states in lung cancer - two-dataset portfolio examining tumor-associated exhaustion in LUAD and its association with anti-PD-1 immunotherapy response in NSCLC.

Modeling the Tumor Microenvironment (TME) as a many-body gravitational system. A synthetic data engine that applies astrophysics principles (N-Body dynamics) to simulate immune-tumor topology and generate ground-truth spatial data.

Spatial fractional reaction-diffusion model optimizing CAR-T immunotherapy for glioblastoma with tumor microenvironment integration