tumor-microenvironment

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology. https://iobr.github.io/IOBR/

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.

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

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

Production framework for 10x Visium, Xenium, and MERFISH spatial transcriptomics. Includes Squidpy spatial neighborhood analysis, ligand-receptor cell communication, and WebGL overlays.

An R package for modeling asymmetric spatial associations between cell types in tissue images using a multilevel Bayesian framework.

End-to-end CODEX multiplex IF analysis pipeline that includes cell segmentation, phenotyping, and spatial neighborhood analysis on the Schürch/Nolan CRC dataset

Code for IN-DEPTH

End-to-end scRNA-seq + AI pipeline for melanoma TME biomarker discovery. CD79A validated in TCGA-SKCM (n=314, Log-Rank p=0.0044, +18.1 months OS).

Distinct mesenchymal cell states mediate prostate cancer progression

When can a clinician trust a spatial immune score? A rigorous reproducibility + trust study on a real MIBI-TOF TNBC cohort: reproduce the classic mixing score, show where it breaks, and abstain on out-of-distribution patients.

Code and data-access documentation for spatially resolved ferroptosis-associated states in glioblastoma.

Developed ML algorisms on transcriptomics landscapes identi-fies SPON1 and ALDH1A2 as candidate prognostic biomarkers in TME and serous ovarian cancer progression

Immune-compartment secretory and regulatory programmes distinguishing checkpoint response in melanoma - single-cell and bulk RNA-seq analysis