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  1. single-cell-tutorial 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 473

  2. single-cell-best-practices single-cell-best-practices Public

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

    Jupyter Notebook 892 212

  3. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 438 106

  4. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 380 50

  5. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 362 59

  6. scib scib Public

    Benchmarking analysis of data integration tools

    Python 348 67

Repositories

Showing 10 of 229 repositories
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 284 Apache-2.0 24 42 1 Updated Apr 29, 2025
  • regvelo Public

    inferring regulatory cellular dynamics

    theislab/regvelo’s past year of commit activity
    Python 40 BSD-3-Clause 1 1 0 Updated Apr 29, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 5 Apache-2.0 1 20 3 Updated Apr 29, 2025
  • theislab/pertpy-reproducibility’s past year of commit activity
    Jupyter Notebook 3 Apache-2.0 2 0 0 Updated Apr 29, 2025
  • theislab/single-cell-best-practices’s past year of commit activity
    Jupyter Notebook 892 212 68 4 Updated Apr 28, 2025
  • jump-cpg0016-segmentation Public

    Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium

    theislab/jump-cpg0016-segmentation’s past year of commit activity
    Jupyter Notebook 8 MIT 0 1 0 Updated Apr 28, 2025
  • scanpydoc Public

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

    theislab/scanpydoc’s past year of commit activity
    Python 12 GPL-3.0 6 2 0 Updated Apr 28, 2025
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate’s past year of commit activity
    Python 22 BSD-3-Clause 7 4 2 Updated Apr 28, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 23 4 42 12 Updated Apr 28, 2025
  • theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 3 BSD-3-Clause 1 25 3 Updated Apr 28, 2025