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  1. single-cell-tutorial Public

    Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

    Jupyter Notebook 1.5k 475

  2. single-cell-best-practices Public

    https://www.sc-best-practices.org

    Jupyter Notebook 903 214

  3. scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 441 106

  4. cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 382 50

  5. scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 363 59

  6. scib Public

    Benchmarking analysis of data integration tools

    Python 348 68

Repositories

Showing 10 of 230 repositories
  • ehrdata Public

    A datastructure for EHR data

    Python 5 Apache-2.0 1 16 2 Updated May 13, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    Python 33 4 43 14 Updated May 13, 2025
  • mapqc Public
    Python 0 MIT 1 2 2 Updated May 13, 2025
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 290 Apache-2.0 24 40 1 Updated May 13, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    Python 132 GPL-3.0 19 14 1 Updated May 13, 2025
  • scanpydoc Public

    Collection of Sphinx extensions similar to (but more flexible than) numpydoc

    Python 12 GPL-3.0 6 2 0 Updated May 13, 2025
  • Jupyter Notebook 903 214 68 4 Updated May 13, 2025
  • troutpy Public

    Package for the analysis of Transcripts outside segmented cells in ST data

    Jupyter Notebook 0 BSD-3-Clause 0 0 1 Updated May 12, 2025
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    Python 23 BSD-3-Clause 7 4 2 Updated May 12, 2025
  • Jupyter Notebook 3 BSD-3-Clause 1 25 3 Updated May 12, 2025