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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 471

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

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

    Jupyter Notebook 856 205

  3. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 430 105

  4. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 372 48

  5. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 355 53

  6. scib scib Public

    Benchmarking analysis of data integration tools

    Python 337 66

Repositories

Showing 10 of 221 repositories
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 279 Apache-2.0 23 43 2 Updated Mar 12, 2025
  • ehrapy-tutorials Public

    Tutorials for ehrapy

    theislab/ehrapy-tutorials’s past year of commit activity
    Jupyter Notebook 9 Apache-2.0 2 0 1 Updated Mar 12, 2025
  • theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 0 25 2 Updated Mar 12, 2025
  • archmap_data Public
    theislab/archmap_data’s past year of commit activity
    Python 1 0 1 1 Updated Mar 12, 2025
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 3 0 0 0 Updated Mar 12, 2025
  • cell_flow_perturbation Public

    Modeling complex perturbations with CellFlow

    theislab/cell_flow_perturbation’s past year of commit activity
    Python 5 2 37 12 Updated Mar 12, 2025
  • archmap_doc Public
    theislab/archmap_doc’s past year of commit activity
    Python 0 0 0 0 Updated Mar 12, 2025
  • theislab/single-cell-best-practices’s past year of commit activity
    Jupyter Notebook 856 205 70 3 Updated Mar 12, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 5 Apache-2.0 1 20 2 Updated Mar 11, 2025
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 140 BSD-3-Clause 9 37 4 Updated Mar 11, 2025

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