Repositories list

• mintflow-reproducibility

  Public
  Reproducible analyses for the MintFlow manuscript

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•6•0•0•Updated Feb 19, 2026Feb 19, 2026

• mintflow

  Public
  Generation of disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data

  deep-learninggraph-neural-networksspatial-transcriptomics+ 1flow-matching

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•24•2•1•Updated Feb 19, 2026Feb 19, 2026

• SP-FM

  Public
  MixFlow: Mixture-Conditioned Flow Matching for Out-of-Distribution Generalization

  Python

  •

  MIT License

  •1•4•0•0•Updated Feb 13, 2026Feb 13, 2026

• nichecompass

  Public
  End-to-end analysis of spatial multi-omics data

  deep-learningvariational-autoencodergraph-neural-networks+ 1spatial-omics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •16•103•10•0•Updated Jan 26, 2026Jan 26, 2026

• CellDISECT

  Public
  Fairness in single-cell data

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•17•0•0•Updated Nov 23, 2025Nov 23, 2025

• stemo

  Public
  Spatial Transcriptomics Embedding Model

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 12, 2025Nov 12, 2025

• nichecompass-reproducibility

  Public
  Reproducible analyses for the NicheCompass manuscript

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •2•13•1•0•Updated Jul 3, 2025Jul 3, 2025

• Loki

  Public
  A visual–omics foundation model to bridge histopathology with spatial transcriptomics

  Python

  •13•0•0•0•Updated Jun 3, 2025Jun 3, 2025

• UNI

  Public
  Pathology Foundation Model - Nature Medicine

  Jupyter Notebook

  •

  Other

  •83•0•0•0•Updated Mar 26, 2025Mar 26, 2025

• geneformer

  Public
  Jupyter Notebook

  •15•1•0•0•Updated Nov 27, 2023Nov 27, 2023