Theis Lab

Institute of Computational Biology

Munich

Pinned Repositories

cellrank
CellRank: dynamics from multi-view single-cell data
Language:Python393 8 74650
dca
Deep count autoencoder for denoising scRNA-seq data
Language:Python262 10 6072
ehrapy
Electronic Health Record Analysis with Python.
Language:Python307 4 34536
scarches
Reference mapping for single-cell genomics
Language:Jupyter Notebook382 11 18663
scgen
Single cell perturbation prediction
Language:Python315 8 8165
scib
Benchmarking analysis of data integration tools
Language:Python379 12 18870
scvelo
RNA Velocity generalized through dynamical modeling
Language:Python466 12 811109
single-cell-best-practices
https://www.sc-best-practices.org
Language:Jupyter Notebook1k 17 237232
single-cell-transformer-papers
Language:HTML325 13 5840
single-cell-tutorial
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"
Language:Jupyter Notebook1.5k 47 101477

Theis Lab's Repositories

theislab/cellrank
CellRank: dynamics from multi-view single-cell data
Language:Python393 8 74650
theislab/ehrapy
Electronic Health Record Analysis with Python.
Language:Python307 4 34536
theislab/moscot
Multi-omic single-cell optimal transport tools
Language:Python172 3 38711
theislab/anndata2ri
Convert between AnnData and SingleCellExperiment
Language:Python139 6 8919
theislab/CellFlow
Modeling complex perturbations with CellFlow
Language:Python8514
theislab/regvelo
inferring regulatory cellular dynamics
Language:Python56 2 155
theislab/DRVI
Unsupervised Deep Disentangled Representation of Single-Cell Omics
Language:Python48 1 54
theislab/spapros
Python package for Probe set selection for targeted spatial transcriptomics.
Language:Python43 3 397
theislab/prophet
Language:Jupyter Notebook36 3 52
theislab/multigrate
Multigrate: multiomic data integration for single-cell genomics
Language:Python27 1 128
theislab/hadge
Comprehensive pipeline for donor demultiplexing in single cell
Language:Nextflow24 3 328
theislab/CFGen
Language:Jupyter Notebook23 1 25
theislab/cross_system_integration
Language:Jupyter Notebook13 2 112
theislab/scanpydoc
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
Language:Python12 5 376
theislab/ehrapy-tutorials
Tutorials for ehrapy
Language:Jupyter Notebook9 2 92
theislab/mapqc
MapQC - a metric for the evaluation of single-cell query-to-reference mappings
Language:Python91
theislab/regvelo_reproducibility
Language:Jupyter Notebook8 0 29
theislab/ehrdata
A datastructure for EHR data
Language:Python7 2 373
theislab/FlatVI
Language:Jupyter Notebook61
theislab/gh-dashboard
A dashboard of everything in the theislab GitHub repository
Language:HTML6 2 0
theislab/multimil_reproducibility
Language:Jupyter Notebook6 3 71
theislab/scProtVelo
Language:Jupyter Notebook5 1 01
theislab/spatialdata-db
Language:Jupyter Notebook5 1 261
theislab/scproto
Interpretable self-supervised prototype learning for denoising and integrating single-cell transcriptomic data via biologically meaningful metacells.
Language:Jupyter Notebook41
theislab/archmap_data
Language:Python1 0 10
theislab/idtrack
Cross-Temporal and Cross-Database Biological Identifier Mapping
Language:Python1 1 0
theislab/tardis
Language:Jupyter Notebook1 1 22
theislab/devVI
Integration of developmental scRNA-seq data
Language:Python01
theislab/2025_cpmeasure_performance_eval
theislab/troutpy
Package for the analysis of Transcripts outside segmented cells in ST data
Language:Jupyter Notebook