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@prism-oncology

PRISM Institute

National PRecISion Medicine Center in Oncology
README.md

👋 Welcome to the PRISM Institute!

The PRISM Institute is a French interdisciplinary institute for precision oncology, established as a modern consortium at the interface of clinical medicine, mathematical modeling, and computational science.

PRISM is an initiative of Gustave Roussy, CentraleSupélec, Université Paris-Saclay, Inserm, and UNICANCER.

Our research combines 🧬 multi-omics profiling, 🔬 computational pathology, and 🤖 clinical AI to decode tumor heterogeneity and support personalized treatment decisions. We develop open-source tools and models that span the full translational arc, from raw molecular data to clinical decision support.

This GitHub organization hosts the software, datasets, and reproducible pipelines associated with our publications and ongoing projects. We are committed to open and reproducible science 🌍. Contributions, issues, and collaborations are welcome — feel free to open an issue or reach out.

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  1. sopa sopa Public

    Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

    Python 274 48

  2. novae novae Public

    Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

    Python 127 12

  3. scyan scyan Public

    Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.

    Python 43 2

Repositories

Showing 6 of 6 repositories
  • novae Public

    Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

    prism-oncology/novae’s past year of commit activity
    Python 127 BSD-3-Clause 12 4 0 Updated Apr 17, 2026
  • sopa Public

    Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

    prism-oncology/sopa’s past year of commit activity
    Python 274 BSD-3-Clause 48 29 1 Updated Apr 17, 2026
  • novae_benchmark Public

    Repository used for the Novae benchmark

    prism-oncology/novae_benchmark’s past year of commit activity
    Python 2 BSD-3-Clause 0 0 0 Updated Apr 17, 2026
  • scyan Public

    Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.

    prism-oncology/scyan’s past year of commit activity
    Python 43 BSD-3-Clause 2 2 0 Updated Apr 8, 2026
  • .github Public

    .github repository

    prism-oncology/.github’s past year of commit activity
    0 0 0 0 Updated Apr 7, 2026
  • scyan_data Public

    Auxiliary repository to store public cytometry datasets and Scyan tables.

    prism-oncology/scyan_data’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Apr 7, 2026

People

This organization has no public members. You must be a member to see who’s a part of this organization.

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