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
•198•826•69•4•Updated Jan 25, 2025Jan 25, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Jan 25, 2025Jan 25, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Jan 25, 2025Jan 25, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Jan 25, 2025Jan 25, 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•259•42•1•Updated Jan 24, 2025Jan 24, 2025
chemCPA
Public
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
genomics drug-discovery transfer-learning single-cell perturbation disentanglement
Jupyter Notebook
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MIT License
•24•105•13•0•Updated Jan 24, 2025Jan 24, 2025
scib-pipeline
Public
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
Python
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MIT License
•27•68•12•4•Updated Jan 23, 2025Jan 23, 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
•9•126•36•4•Updated Jan 22, 2025Jan 22, 2025
moscot_notebooks
Public
Analysis notebooks using the moscot package
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•4•8•3•2•Updated Jan 22, 2025Jan 22, 2025
spatialdata-db
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•25•0•Updated Jan 22, 2025Jan 22, 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 22, 2025Jan 22, 2025
ehrdata
Public
A datastructure for EHR data
Python
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Apache License 2.0
•1•5•21•2•Updated Jan 21, 2025Jan 21, 2025
single-cell-transformer-papers
Public
HTML
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Other
•37•289•43•0•Updated Jan 21, 2025Jan 21, 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•26•1•0•Updated Jan 21, 2025Jan 21, 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
•16•130•13•0•Updated Jan 21, 2025Jan 21, 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 Jan 21, 2025Jan 21, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•6•17•4•2•Updated Jan 20, 2025Jan 20, 2025
DRVI
Public
Unsupervised Deep Disentangled Representation of Single-Cell Omics
python bioinformatics integration transcriptomics single-cell disentanglement anndata
Python
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BSD 3-Clause "New" or "Revised" License
•3•35•2•1•Updated Jan 20, 2025Jan 20, 2025
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 Jan 15, 2025Jan 15, 2025
scib
Public
Benchmarking analysis of data integration tools
Python
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MIT License
•64•325•34•6•Updated Jan 14, 2025Jan 14, 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
•52•348•48•7•Updated Jan 11, 2025Jan 11, 2025
IMPA
Public
Jupyter Notebook
•1•10•0•0•Updated Jan 10, 2025Jan 10, 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
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BSD 3-Clause "New" or "Revised" License
•0•4•0•0•Updated Jan 7, 2025Jan 7, 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•78•16•0•Updated Jan 6, 2025Jan 6, 2025
prophet
Public
Python
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MIT License
•2•27•3•0•Updated Dec 22, 2024Dec 22, 2024
moscot-framework_reproducibility
Public
Data analysis for the moscot-framework project
Jupyter Notebook
•0•6•1•0•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
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•359•19•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•157•12•1•Updated Dec 10, 2024Dec 10, 2024