Theis Lab

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249 repositories

cellucid
Public
Interactive 3D UMAP viewer that scales to massive datasets.
JavaScript
•
Other
•0•2•0•0•Updated Dec 20, 2025Dec 20, 2025
huCIRA
Public
Python
•
MIT License
•3•21•1•0•Updated Dec 20, 2025Dec 20, 2025
hadge
Public
Comprehensive pipeline for donor demultiplexing in single cell
single-cell deconvolution demultiplexing
Nextflow
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MIT License
•7•24•24•1•Updated Dec 20, 2025Dec 20, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•8•1•0•Updated Dec 20, 2025Dec 20, 2025
ehrdata
Public
A datastructure for EHR data
data-analysis ehr ehrapy
Python
•
Apache License 2.0
•4•8•17•1•Updated Dec 19, 2025Dec 19, 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
•38•323•30•0•Updated Dec 19, 2025Dec 19, 2025
cellink
Public
Scalable framework for integrating single-cell omics with genetic data using AnnData.
genetics single-cell anndata
Python
•
Apache License 2.0
•0•6•11•2•Updated Dec 19, 2025Dec 19, 2025
prophet
Public
Python
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MIT License
•3•38•6•0•Updated Dec 18, 2025Dec 18, 2025
single-cell-best-practices
Public
https://www.sc-best-practices.org
tutorial rna-seq book single-cell
Jupyter Notebook
•
Other
•246•1.1k•77•2•Updated Dec 17, 2025Dec 17, 2025
multimil
Public
Weakly supervised learning uncovers phenotypic signatures in single-cell data
Python
•
BSD 3-Clause "New" or "Revised" License
•7•36•3•1•Updated Dec 17, 2025Dec 17, 2025
perturbation-metrics
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•7•0•1•Updated Dec 16, 2025Dec 16, 2025
HumanCytokineDict
Public
Human Cytokine Dictionary
Jupyter Notebook
•2•1•0•1•Updated Dec 16, 2025Dec 16, 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•143•13•0•Updated Dec 16, 2025Dec 16, 2025
scanpydoc
Public
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
Python
•
GNU General Public License v3.0
•5•11•3•0•Updated Dec 16, 2025Dec 16, 2025
troutpy
Public
Package for the analysis of Transcripts outside segmented cells in ST data
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•2•23•0•2•Updated Dec 15, 2025Dec 15, 2025
moscot
Public
Multi-omic single-cell optimal transport tools
single-cell optimal-transport
Python
•
BSD 3-Clause "New" or "Revised" License
•13•182•30•5•Updated Dec 15, 2025Dec 15, 2025
spatialdata-db
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•1•10•26•3•Updated Dec 15, 2025Dec 15, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•9•30•5•2•Updated Dec 15, 2025Dec 15, 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
•4•56•7•2•Updated Dec 15, 2025Dec 15, 2025
mapqc
Public
MapQC - a metric for the evaluation of single-cell query-to-reference mappings
integration mapping transcriptomics single-cell atlas query-to-reference-mapping
Python
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MIT License
•1•11•0•1•Updated Dec 15, 2025Dec 15, 2025
CellFlow
Public
Modeling complex perturbations with CellFlow
Python
•
Other
•16•104•49•14•Updated Dec 15, 2025Dec 15, 2025
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
•
Apache License 2.0
•2•9•0•0•Updated Dec 15, 2025Dec 15, 2025
zellkonverter
Public
Conversion between scRNA-seq objects
r conversion bioconductor scrna-seq
R
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Other
•31•194•13•2•Updated Dec 15, 2025Dec 15, 2025
cellucid-python
Public
Tools to export data into the Cellucid web viewer’s manifest and binaries.
Python
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Dec 15, 2025Dec 15, 2025
CellFlow2
Public
Modeling complex perturbations with CellFlow
Python
•
Other
•0•5•0•0•Updated Dec 13, 2025Dec 13, 2025
scConcept
Public
Contrastive pre-training for technology-agnostic single-cell representations beyond reconstruction
Python
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MIT License
•3•18•1•0•Updated Dec 12, 2025Dec 12, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Dec 9, 2025Dec 9, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Dec 9, 2025Dec 9, 2025
CellHermes
Public
LoRA finetuned LLM for single cell genomics research
Python
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GNU General Public License v3.0
•0•8•1•0•Updated Dec 3, 2025Dec 3, 2025
scarches
Public
Reference mapping for single-cell genomics
deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•66•396•56•9•Updated Dec 2, 2025Dec 2, 2025