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    230 repositories

    • single-cell-best-practices

      Public
      https://www.sc-best-practices.org
      tutorialrna-seqbooksingle-cell
      Jupyter Notebook
      •
      Other
      •214•904•69•4•Updated May 14, 2025May 14, 2025

    • ehrdata

      Public
      A datastructure for EHR data
      Python
      •
      Apache License 2.0
      •1•5•17•2•Updated May 13, 2025May 13, 2025

    • CellFlow

      Public
      Modeling complex perturbations with CellFlow
      Python
      •
      Other
      •5•34•43•14•Updated May 13, 2025May 13, 2025

    • mapqc

      Public
      Python
      •
      MIT License
      •1•0•2•2•Updated May 13, 2025May 13, 2025

    • ehrapy

      Public
      Electronic Health Record Analysis with Python.
      ehrelectronic-health-recordscverseelectronic-medical-record
      Python
      •
      Apache License 2.0
      •24•290•40•1•Updated May 13, 2025May 13, 2025

    • anndata2ri

      Public
      Convert between AnnData and SingleCellExperiment
      jupyterbioconductorsingle-cellrpy2scanpy
      Python
      •
      GNU General Public License v3.0
      •19•132•14•1•Updated May 13, 2025May 13, 2025

    • scanpydoc

      Public
      Collection of Sphinx extensions similar to (but more flexible than) numpydoc
      Python
      •
      GNU General Public License v3.0
      •6•12•2•0•Updated May 13, 2025May 13, 2025

    • troutpy

      Public
      Package for the analysis of Transcripts outside segmented cells in ST data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated May 12, 2025May 12, 2025

    • multigrate

      Public
      Multigrate: multiomic data integration for single-cell genomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•24•4•2•Updated May 12, 2025May 12, 2025

    • spatialdata-db

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•25•3•Updated May 12, 2025May 12, 2025

    • DRVI

      Public
      Unsupervised Deep Disentangled Representation of Single-Cell Omics
      pythonbioinformaticsintegrationtranscriptomicssingle-celldisentanglementanndata
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•42•5•1•Updated May 12, 2025May 12, 2025

    • moscot

      Public
      Multi-omic single-cell optimal transport tools
      single-celloptimal-transport
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•153•35•6•Updated May 12, 2025May 12, 2025

    • devVI

      Public
      Integration of developmental scRNA-seq data
      Python
      •
      MIT License
      •1•0•0•1•Updated May 12, 2025May 12, 2025

    • archmap_data

      Public
      Python
      •0•1•1•1•Updated May 12, 2025May 12, 2025

    • txsim

      Public
      Python
      •1•3•36•4•Updated May 12, 2025May 12, 2025

    • moscot_notebooks

      Public
      Analysis notebooks using the moscot package
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•8•5•3•Updated May 11, 2025May 11, 2025

    • regvelo

      Public
      inferring regulatory cellular dynamics
      generative-modelrna-velocity-estimationperturbation-analysisgrn-inferencesingle-cell-dynamics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•41•1•0•Updated May 8, 2025May 8, 2025

    • archmap_doc

      Public
      Python
      •0•0•0•0•Updated May 8, 2025May 8, 2025

    • pertpy-reproducibility

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •2•3•0•0•Updated May 7, 2025May 7, 2025

    • gh-dashboard

      Public
      A dashboard of everything in the theislab GitHub repository
      HTML
      •0•5•0•0•Updated May 6, 2025May 6, 2025

    • prophet

      Public
      Jupyter Notebook
      •
      MIT License
      •2•31•2•0•Updated May 5, 2025May 5, 2025

    • vevo_Tahoe_100m_analysis

      Public
      Jupyter Notebook
      •3•22•3•2•Updated May 5, 2025May 5, 2025

    • jump-cpg0016-segmentation

      Public
      Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium
      Jupyter Notebook
      •
      MIT License
      •0•8•1•0•Updated Apr 28, 2025Apr 28, 2025

    • ehrapy-tutorials

      Public
      Tutorials for ehrapy
      Jupyter Notebook
      •
      Apache License 2.0
      •2•9•1•0•Updated Apr 27, 2025Apr 27, 2025

    • cellrank_protocol

      Public
      Repository accompanying CellRank's Nature Protocols article.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • cellflow_reproducibility

      Public
      Reproducibility repository for CellFlow
      Jupyter Notebook
      •2•1•0•0•Updated Apr 23, 2025Apr 23, 2025

    • scproto

      Public
      Interpretable self-supervised prototype learning for denoising and integrating single-cell transcriptomic data via biologically meaningful metacells.
      Jupyter Notebook
      •1•2•0•0•Updated Apr 21, 2025Apr 21, 2025

    • zellkonverter

      Public
      Conversion between scRNA-seq objects
      rconversionscrna-seqbioconductor
      R
      •
      Other
      •29•174•12•1•Updated Apr 19, 2025Apr 19, 2025

    • multimil

      Public
      Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•32•9•1•Updated Apr 15, 2025Apr 15, 2025

    • CFGen

      Public
      Jupyter Notebook
      •
      MIT License
      •5•13•0•0•Updated Apr 14, 2025Apr 14, 2025
    0