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    272 repositories

    • cellucid-python

      Public
      The complete Python toolkit for Cellucid. Serve, export, document, explore.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Jul 30, 2026Jul 30, 2026

    • cellucid-demo-custom-datasets

      Public
      User dataset exports demo for the Cellucid web app.
      Python
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • cellucid-r

      Public
      From R to exploration in Cellucid. One function, minimal footprint.
      R
      •
      Other
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • cellucid

      Public
      See every cell. Query any gene. Fly through millions. Zero friction.
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Jul 30, 2026Jul 30, 2026

    • sckitflow

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•20•8•Updated Jul 30, 2026Jul 30, 2026

    • cellucid-annotation

      Public template
      From clusters to consensus. Collaborative cell type annotation for Cellucid.
      Python
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • cellucid-datasets

      Public
      Sample dataset exports for the Cellucid web app, hosted separately to keep the app lightweight and allow independent dataset updates.
      Python
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • scfit

      Public
      Python
      •
      MIT License
      •0•1•1•1•Updated Jul 30, 2026Jul 30, 2026

    • gh-dashboard

      Public
      A dashboard of everything in the theislab GitHub repository
      HTML
      •0•8•1•0•Updated Jul 30, 2026Jul 30, 2026

    • imseq-analysis

      Public
      Collaboration of Theis lab with MPG on im-seq assay (brightfield imaging and transcriptomics)
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • single-cell-best-practices

      Public
      https://www.sc-best-practices.org
      tutorialrna-seqbook
      tutorialrna-seqbooksingle-cell
      Jupyter Notebook
      •
      Other
      •278•1.2k•57•2•Updated Jul 29, 2026Jul 29, 2026

    • interscale

      Public
      InterScale: multi-scale cellular interaction analysis model for spatial transcriptomics
      spatial-transcriptomicsgraph-transformercell-cell-communication
      spatial-transcriptomicsgraph-transformercell-cell-communication
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•11•8•3•Updated Jul 29, 2026Jul 29, 2026

    • DRVI

      Public
      Unsupervised Deep Disentangled Representation of Single-Cell Omics
      pythonbioinformaticsintegration
      pythonbioinformaticsintegrationtranscriptomicssingle-celldisentanglementanndata
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•72•5•2•Updated Jul 29, 2026Jul 29, 2026

    • cellink

      Public
      Scalable framework for integrating single-cell omics with genetic data using AnnData.
      geneticssingle-cellanndata
      geneticssingle-cellanndata
      Python
      •
      Apache License 2.0
      •5•20•6•1•Updated Jul 29, 2026Jul 29, 2026

    • anndata2ri

      Public
      Convert between AnnData and SingleCellExperiment
      jupyterbioconductorsingle-cell
      jupyterbioconductorsingle-cellrpy2scanpy
      Python
      •
      GNU General Public License v3.0
      •19•152•11•0•Updated Jul 28, 2026Jul 28, 2026

    • scanpydoc

      Public
      Collection of Sphinx extensions similar to (but more flexible than) numpydoc
      Python
      •
      GNU General Public License v3.0
      •5•12•4•0•Updated Jul 28, 2026Jul 28, 2026

    • spatialdata-db

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•12•26•3•Updated Jul 27, 2026Jul 27, 2026

    • troutpy

      Public
      Package for the analysis of Transcripts outside segmented cells in ST data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•31•0•2•Updated Jul 27, 2026Jul 27, 2026

    • moscot

      Public
      Multi-omic single-cell optimal transport tools
      single-celloptimal-transport
      single-celloptimal-transport
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •16•214•31•5•Updated Jul 27, 2026Jul 27, 2026

    • mapqc

      Public
      MapQC - a metric for the evaluation of single-cell query-to-reference mappings
      integrationmappingtranscriptomics
      integrationmappingtranscriptomicssingle-cellatlasquery-to-reference-mapping
      Python
      •
      MIT License
      •1•12•0•2•Updated Jul 27, 2026Jul 27, 2026

    • multigrate

      Public
      Multigrate: multiomic data integration for single-cell genomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•34•2•2•Updated Jul 27, 2026Jul 27, 2026

    • ehrdata

      Public
      A datastructure for EHR data
      data-analysisehrehrapy
      data-analysisehrehrapy
      Python
      •
      Apache License 2.0
      •6•15•10•3•Updated Jul 27, 2026Jul 27, 2026

    • CellFlow

      Public
      Modeling complex perturbations with CellFlow
      Python
      •
      MIT License
      •27•152•50•18•Updated Jul 27, 2026Jul 27, 2026

    • ehrapy

      Public
      Electronic Health Record Analysis with Python.
      ehrelectronic-health-recordscverse
      ehrelectronic-health-recordscverseelectronic-medical-record
      Python
      •
      Apache License 2.0
      •50•356•15•4•Updated Jul 27, 2026Jul 27, 2026

    • CFGen

      Public
      Jupyter Notebook
      •
      MIT License
      •5•37•0•0•Updated Jul 27, 2026Jul 27, 2026

    • Chem-PerturBridge_analysis

      Public
      Jupyter Notebook
      •1•0•0•1•Updated Jul 27, 2026Jul 27, 2026

    • ReconEval

      Public
      Benchmarking for gene expression from single cell latent representations
      Jupyter Notebook
      •
      MIT License
      •2•19•0•0•Updated Jul 26, 2026Jul 26, 2026

    • ehrapy-tutorials

      Public
      Tutorials for ehrapy
      Jupyter Notebook
      •
      Apache License 2.0
      •2•9•0•1•Updated Jul 25, 2026Jul 25, 2026

    • embpy

      Public
      Python
      •
      MIT License
      •1•20•9•2•Updated Jul 25, 2026Jul 25, 2026

    • chem-perturbridge_lpm

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 24, 2026Jul 24, 2026
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