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@theislab

Theis Lab

Institute of Computational Biology

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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 1.3k 449

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

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

    Jupyter Notebook 719 166

  3. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 405 102

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 326 51

  5. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 337 44

  6. scib scib Public

    Benchmarking analysis of data integration tools

    Python 285 62

Repositories

Showing 10 of 206 repositories
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 1 0 0 0 Updated Aug 18, 2024
  • masterpraktikum_ssl_segmentation Public

    Repository accompanying the 2024 Masterpraktikum Project: Integrative Analysis of Histological Images and Gene Expression Data for Pathological Region Classification

    theislab/masterpraktikum_ssl_segmentation’s past year of commit activity
    2 2 0 0 Updated Aug 18, 2024
  • mubind Public

    Learning motif contributions to cell transitions using sequence features and graphs.

    theislab/mubind’s past year of commit activity
    Python 22 MIT 0 30 0 Updated Aug 17, 2024
  • cellrank Public

    CellRank: dynamics from multi-view single-cell data

    theislab/cellrank’s past year of commit activity
    Python 337 BSD-3-Clause 44 17 0 Updated Aug 16, 2024
  • prophet Public
    theislab/prophet’s past year of commit activity
    Python 2 0 0 0 Updated Aug 16, 2024
  • cpa Public

    The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

    theislab/cpa’s past year of commit activity
    Python 80 BSD-3-Clause 18 18 1 Updated Aug 14, 2024
  • prophet-reproducibility Public
    theislab/prophet-reproducibility’s past year of commit activity
    0 0 0 0 Updated Aug 13, 2024
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 123 GPL-3.0 16 14 1 Updated Aug 13, 2024
  • 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 3 0 Updated Aug 13, 2024
  • graphcompass Public

    GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems

    theislab/graphcompass’s past year of commit activity
    Jupyter Notebook 26 MIT 0 1 0 Updated Aug 13, 2024
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