This repository contains software and analysis code used for the publication:
A Compendium of Next-Generation Patient-Derived Models for Diverse Cancer Types
The Human Cancer Models Initiative (HCMI) is an international consortium generating next-generation patient-derived cancer models with matched molecular and clinical data. The initiative expands disease representation and provides standardized, deeply characterized tumor-derived models to support research and translational discovery.
More about HCMI
Public and controlled-access data, including WGS/WES, RNA-seq, DNA methylation, WSIs, and clinical metadata, are available from the NCI Genomic Data Commons (GDC). The HCMI GDC publication page serves as a central reference linking to pre-processed data generated in this study.
This repository includes analysis scripts and pipeline references used to generate the results presented in the HCMI flagship manuscript.
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Analysis Pipelines — Computational workflows for tumor–model concordance and biological distance metrics.
Pipelines are included as submodules and documented at:pipelines/. -
Analysis & Figure Notebooks and Scripts — Data preprocessing, downstream analyses, and figure-generation notebooks and scripts are in:
analyses/. The directory includesnotebooks/andscripts/subdirectories.
The HCMI ecosystem includes multiple platforms for exploring, accessing, and requesting patient-derived models:
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HCMI Searchable Catalogue — primary portal to browse available HCMI models and associated metadata
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HCMI Explorer Suite — interactive viewer for clinical timelines, and genomic annotations.
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cBioPortal (HCMI Collection) — integrated genomic visualization for HCMI models
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HCMI page @ ATCC — models, culturing protocols, and ordering information available through ATCC
To properly check out this repository and ensure all submodules are included, use the following command:
git clone --recurse-submodules https://github.com/NCICCGPO/HCMI-Flagship-Manuscript.gitThis will automatically retrieve all submodules required for the analysis.