Theis Lab

All

229 repositories

CellFlow
Public
Modeling complex perturbations with CellFlow
Python
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Other
•4•12•39•13•Updated Apr 17, 2025Apr 17, 2025
DRVI
Public
Unsupervised Deep Disentangled Representation of Single-Cell Omics
python bioinformatics integration transcriptomics single-cell disentanglement anndata
Python
•
BSD 3-Clause "New" or "Revised" License
•3•39•5•0•Updated Apr 17, 2025Apr 17, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Apr 16, 2025Apr 16, 2025
scproto
Public
Interpretable self-supervised prototype learning for denoising and integrating single-cell transcriptomic data via biologically meaningful metacells.
Jupyter Notebook
•0•0•0•0•Updated Apr 16, 2025Apr 16, 2025
single-cell-best-practices
Public
https://www.sc-best-practices.org
tutorial rna-seq book single-cell
Jupyter Notebook
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Other
•212•884•65•3•Updated Apr 15, 2025Apr 15, 2025
ehrdata
Public
A datastructure for EHR data
Python
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Apache License 2.0
•1•5•19•3•Updated Apr 15, 2025Apr 15, 2025
multimil
Public
Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
Python
•
BSD 3-Clause "New" or "Revised" License
•5•30•9•1•Updated Apr 15, 2025Apr 15, 2025
scanpydoc
Public
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
Python
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GNU General Public License v3.0
•6•12•2•0•Updated Apr 15, 2025Apr 15, 2025
prophet
Public
Python
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MIT License
•2•30•2•1•Updated Apr 15, 2025Apr 15, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•7•20•4•3•Updated Apr 14, 2025Apr 14, 2025
spatialdata-db
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•1•3•25•3•Updated Apr 14, 2025Apr 14, 2025
ehrapy
Public
Electronic Health Record Analysis with Python.
ehr electronic-health-record scverse electronic-medical-record
Python
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Apache License 2.0
•24•283•42•2•Updated Apr 14, 2025Apr 14, 2025
mapqc
Public
Python
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MIT License
•1•0•2•2•Updated Apr 14, 2025Apr 14, 2025
devVI
Public
Integration of developmental scRNA-seq data
Python
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MIT License
•1•0•0•1•Updated Apr 14, 2025Apr 14, 2025
moscot
Public
Multi-omic single-cell optimal transport tools
single-cell optimal-transport
Python
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BSD 3-Clause "New" or "Revised" License
•10•150•35•5•Updated Apr 14, 2025Apr 14, 2025
anndata2ri
Public
Convert between AnnData and SingleCellExperiment
jupyter bioconductor single-cell rpy2 scanpy
Python
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GNU General Public License v3.0
•19•132•14•1•Updated Apr 14, 2025Apr 14, 2025
CFGen
Public
Jupyter Notebook
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MIT License
•5•12•0•0•Updated Apr 14, 2025Apr 14, 2025
cellrank_protocol
Public
Repository accompanying CellRank's Nature Protocols article.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Apr 14, 2025Apr 14, 2025
pertpy-reproducibility
Public
Jupyter Notebook
•
Apache License 2.0
•2•3•0•0•Updated Apr 14, 2025Apr 14, 2025
scaling_flow
Public
CellFlow across datasets, à la Prophet
Python
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Other
•4•0•0•0•Updated Apr 14, 2025Apr 14, 2025
spatial_scooby
Public
spatial_scooby: Modeling spatial transcriptomics from DNA sequence at single-cell resolution.
Python
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MIT License
•3•0•0•0•Updated Apr 11, 2025Apr 11, 2025
graphcompass
Public
GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
Jupyter Notebook
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MIT License
•1•35•2•0•Updated Apr 11, 2025Apr 11, 2025
cellflow_reproducibility
Public
Reproducibility repository for CellFlow
Jupyter Notebook
•2•0•0•0•Updated Apr 11, 2025Apr 11, 2025
zellkonverter
Public
Conversion between scRNA-seq objects
r conversion scrna-seq bioconductor
R
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Other
•29•171•13•1•Updated Apr 10, 2025Apr 10, 2025
tissue
Public
Python
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MIT License
•0•2•0•0•Updated Apr 10, 2025Apr 10, 2025
cellflow_reproducibility_private_backup
Public archive
Private backup reproducibility repository for CellFlow with all branches
Jupyter Notebook
•2•0•0•0•Updated Apr 10, 2025Apr 10, 2025
cellrank
Public
CellRank: dynamics from multi-view single-cell data
data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning single-cell-genomics single-cell-rna-seq cell-fate-transitions
Python
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BSD 3-Clause "New" or "Revised" License
•49•377•20•0•Updated Apr 7, 2025Apr 7, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Apr 5, 2025Apr 5, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Apr 4, 2025Apr 4, 2025
cross_system_integration
Public
Jupyter Notebook
•2•12•11•1•Updated Apr 3, 2025Apr 3, 2025