Theis Lab

Theis Lab at Institute of Computational Biology, Helmholtz Munich

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single-cell-best-practices single-cell-best-practices Public

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

Jupyter Notebook 1.2k 270
scvelo scvelo Public

RNA Velocity generalized through dynamical modeling

Python 501 112
scarches scarches Public

Reference mapping for single-cell genomics

Jupyter Notebook 404 70
scib scib Public

Benchmarking analysis of data integration tools

Python 416 76
ehrapy ehrapy Public

Electronic Health Record Analysis with Python.

Python 350 45
moscot moscot Public

Multi-omic single-cell optimal transport tools

Python 207 16

Repositories

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 9 MIT 0 1 3 Updated May 20, 2026
ehrapy Public
Electronic Health Record Analysis with Python.

theislab/ehrapy’s past year of commit activity

Python 350 Apache-2.0 45 17 4 Updated May 20, 2026
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 May 20, 2026
gh-dashboard Public
A dashboard of everything in the theislab GitHub repository

theislab/gh-dashboard’s past year of commit activity

HTML 8 0 1 0 Updated May 20, 2026
single-cell-best-practices Public
https://www.sc-best-practices.org

theislab/single-cell-best-practices’s past year of commit activity

Jupyter Notebook 1,197 270 71 3 Updated May 20, 2026
cellink Public
Scalable framework for integrating single-cell omics with genetic data using AnnData.

theislab/cellink’s past year of commit activity

Python 16 Apache-2.0 5 8 5 Updated May 19, 2026
anndata2ri Public
Convert between AnnData and SingleCellExperiment

theislab/anndata2ri’s past year of commit activity

Python 150 GPL-3.0 19 13 0 Updated May 19, 2026
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 5 4 0 Updated May 19, 2026
troutpy Public
Package for the analysis of Transcripts outside segmented cells in ST data

theislab/troutpy’s past year of commit activity

Jupyter Notebook 29 BSD-3-Clause 2 0 2 Updated May 18, 2026
multigrate Public
Multigrate: multiomic data integration for single-cell genomics

theislab/multigrate’s past year of commit activity

Python 33 BSD-3-Clause 8 6 2 Updated May 18, 2026

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