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Lotfollahi-lab

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  1. nichecompass nichecompass Public

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

    Python 125 20

  2. terra terra Public

    Spatial transcriptomics foundation model based on Graph Transformer and JEPA

    Python 68 1

  3. Perturbgen Perturbgen Public

    Python 27 8

  4. mintflow mintflow Public template

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

    Python 27 5

  5. tripso tripso Public

    Python 26 1

  6. CellDISECT CellDISECT Public

    Fairness in single-cell data

    Python 21 2

Repositories

Showing 10 of 21 repositories
  • nichecompass Public

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

    Lotfollahi-lab/nichecompass's past year of commit activity
    Python 125 BSD-3-Clause 20 10 0 Updated Sep 14, 2026
  • nichecompass-reproducibility Public

    Reproducible analyses for the NicheCompass manuscript

    Lotfollahi-lab/nichecompass-reproducibility's past year of commit activity
    Jupyter Notebook 14 BSD-3-Clause 3 1 0 Updated Sep 13, 2026
  • mintflow-reproducibility Public

    Reproducible analyses for the MintFlow manuscript

    Lotfollahi-lab/mintflow-reproducibility's past year of commit activity
    Jupyter Notebook 7 BSD-3-Clause 1 0 0 Updated Sep 3, 2026
  • Perturbgen Public
    Lotfollahi-lab/Perturbgen's past year of commit activity
    Python 27 MIT 8 2 1 Updated Sep 2, 2026
  • squint-extended Public Forked from Lotfollahi-lab/squint

    Discrete tokenization for spatial transcriptomics tissue sections

    Lotfollahi-lab/squint-extended's past year of commit activity
    Python 0 MIT 1 0 0 Updated Sep 1, 2026
  • g2t-reproducibility Public

    Graph generation for single-cell RNA sequencing data

    Lotfollahi-lab/g2t-reproducibility's past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Aug 16, 2026
  • g2t Public

    Graph generation for scRNA-seq data

    Lotfollahi-lab/g2t's past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Aug 16, 2026
  • squint-reproducibility Public

    Reproducible analyses for SQUINT

    Lotfollahi-lab/squint-reproducibility's past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Aug 13, 2026
  • terra Public

    Spatial transcriptomics foundation model based on Graph Transformer and JEPA

    Lotfollahi-lab/terra's past year of commit activity
    Python 68 BSD-3-Clause 1 1 0 Updated Aug 10, 2026
  • terra-reproducibility Public

    Reproducible analyses for the TERRA manuscript

    Lotfollahi-lab/terra-reproducibility's past year of commit activity
    Jupyter Notebook 7 BSD-3-Clause 0 2 (2 issues need help) 0 Updated Jul 23, 2026

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