Theis Lab

All

215 repositories

single-cell-best-practices
Public
https://www.sc-best-practices.org
tutorial rna-seq book single-cell
Jupyter Notebook
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Other
•196•813•71•4•Updated Jan 9, 2025Jan 9, 2025
IMPA
Public
Jupyter Notebook
•1•9•0•0•Updated Jan 9, 2025Jan 9, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Jan 9, 2025Jan 9, 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
•22•253•45•2•Updated Jan 9, 2025Jan 9, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Jan 9, 2025Jan 9, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Jan 9, 2025Jan 9, 2025
moscot
Public
Multi-omic single-cell optimal transport tools
single-cell optimal-transport
Python
•
BSD 3-Clause "New" or "Revised" License
•9•119•33•6•Updated Jan 9, 2025Jan 9, 2025
pertpy-reproducibility
Public
Jupyter Notebook
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Apache License 2.0
•1•1•0•0•Updated Jan 8, 2025Jan 8, 2025
regvelo_reproducibility
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•2•0•0•Updated Jan 7, 2025Jan 7, 2025
anndata2ri
Public
Convert between AnnData and SingleCellExperiment
jupyter bioconductor single-cell rpy2 scanpy
Python
•
GNU General Public License v3.0
•16•130•13•0•Updated Jan 7, 2025Jan 7, 2025
scanpydoc
Public
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
Python
•
GNU General Public License v3.0
•6•12•3•0•Updated Jan 7, 2025Jan 7, 2025
troutpy
Public
Package for the analysis of Transcripts outside segmented cells in ST data
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•1•Updated Jan 6, 2025Jan 6, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•6•16•4•2•Updated Jan 6, 2025Jan 6, 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•35•2•1•Updated Jan 6, 2025Jan 6, 2025
ehrdata
Public
A datastructure for EHR data
Python
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Apache License 2.0
•1•5•18•3•Updated Jan 6, 2025Jan 6, 2025
nicheformer
Public
Repository for Nicheformer: a foundation model for single-cell and spatial omics
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•3•76•15•0•Updated Jan 6, 2025Jan 6, 2025
regvelo
Public
inferring regulatory cellular dynamics
generative-model rna-velocity-estimation perturbation-analysis grn-inference single-cell-dynamics
Python
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BSD 3-Clause "New" or "Revised" License
•1•20•0•0•Updated Dec 31, 2024Dec 31, 2024
prophet
Public
Python
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MIT License
•2•27•3•0•Updated Dec 22, 2024Dec 22, 2024
single-cell-transformer-papers
Public
HTML
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Other
•36•289•41•0•Updated Dec 21, 2024Dec 21, 2024
graphcompass
Public
GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
Jupyter Notebook
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MIT License
•0•34•1•0•Updated Dec 21, 2024Dec 21, 2024
moscot-framework_reproducibility
Public
Data analysis for the moscot-framework project
Jupyter Notebook
•0•3•2•0•Updated Dec 20, 2024Dec 20, 2024
scib
Public
Benchmarking analysis of data integration tools
Python
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MIT License
•63•322•34•6•Updated Dec 20, 2024Dec 20, 2024
neural_organoid_atlas
Public
Reproducibility repository for the Human Neural Organoid Atlas publication
Jupyter Notebook
•4•26•2•1•Updated Dec 16, 2024Dec 16, 2024
moscot_notebooks
Public
Analysis notebooks using the moscot package
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•4•8•4•3•Updated Dec 16, 2024Dec 16, 2024
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
•47•356•18•0•Updated Dec 14, 2024Dec 14, 2024
zellkonverter
Public
Conversion between scRNA-seq objects
r conversion scrna-seq bioconductor
R
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Other
•28•156•12•1•Updated Dec 10, 2024Dec 10, 2024
scvelo
Public
RNA Velocity generalized through dynamical modeling
Python
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BSD 3-Clause "New" or "Revised" License
•104•421•58•2•Updated Dec 9, 2024Dec 9, 2024
scgen
Public
Single cell perturbation prediction
bioinformatics deep-learning generative-model scrna-seq transcriptomics single-cell single-cell-genomics
Python
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GNU General Public License v3.0
•56•277•23•5•Updated Dec 5, 2024Dec 5, 2024
spatialdata-db
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•25•0•Updated Dec 2, 2024Dec 2, 2024
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
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Apache License 2.0
•1•8•0•0•Updated Dec 1, 2024Dec 1, 2024