Theis Lab

All

216 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
•199•838•68•6•Updated Feb 16, 2025Feb 16, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Feb 16, 2025Feb 16, 2025
pertpy-reproducibility
Public
Jupyter Notebook
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Apache License 2.0
•1•2•0•2•Updated Feb 16, 2025Feb 16, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Feb 16, 2025Feb 16, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Feb 15, 2025Feb 15, 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•261•43•2•Updated Feb 14, 2025Feb 14, 2025
archmap_doc
Public
Python
•0•0•0•0•Updated Feb 14, 2025Feb 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
•9•132•33•5•Updated Feb 14, 2025Feb 14, 2025
single-cell-transformer-papers
Public
HTML
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Other
•39•294•39•0•Updated Feb 14, 2025Feb 14, 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
•
BSD 3-Clause "New" or "Revised" License
•48•366•20•1•Updated Feb 13, 2025Feb 13, 2025
spatialdata-db
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•25•1•Updated Feb 13, 2025Feb 13, 2025
inVAE_reproducibility
Public
Jupyter Notebook
•0•0•0•0•Updated Feb 13, 2025Feb 13, 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•36•1•0•Updated Feb 12, 2025Feb 12, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•6•18•4•1•Updated Feb 12, 2025Feb 12, 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
•17•132•13•0•Updated Feb 11, 2025Feb 11, 2025
ehrdata
Public
A datastructure for EHR data
Python
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Apache License 2.0
•1•5•20•1•Updated Feb 11, 2025Feb 11, 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 Feb 11, 2025Feb 11, 2025
deconvATAC
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•2•Updated Feb 8, 2025Feb 8, 2025
jump-cpg0016-segmentation
Public
Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium
Jupyter Notebook
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MIT License
•0•8•0•0•Updated Feb 6, 2025Feb 6, 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
•25•105•6•1•Updated Feb 6, 2025Feb 6, 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•5•3•Updated Feb 5, 2025Feb 5, 2025
MS_mv_modelling
Public
A deep generative model for single-cell MS proteomics data
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•1•1•0•0•Updated Feb 5, 2025Feb 5, 2025
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
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Apache License 2.0
•1•9•0•0•Updated Feb 5, 2025Feb 5, 2025
scib-pipeline
Public
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
Python
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MIT License
•28•68•12•4•Updated Jan 23, 2025Jan 23, 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•33•0•0•Updated Jan 21, 2025Jan 21, 2025
graphcompass
Public
GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
Jupyter Notebook
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MIT License
•1•35•1•0•Updated Jan 15, 2025Jan 15, 2025
scib
Public
Benchmarking analysis of data integration tools
Python
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MIT License
•65•332•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•49•7•Updated Jan 11, 2025Jan 11, 2025
IMPA
Public
Jupyter Notebook
•1•12•0•0•Updated Jan 10, 2025Jan 10, 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