Theis Lab

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215 repositories

troutpy
Public
Package for the analysis of Transcripts outside segmented cells in ST data
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•1•Updated Jan 3, 2025Jan 3, 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 2, 2025Jan 2, 2025
regvelo_reproducibility
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jan 2, 2025Jan 2, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Jan 2, 2025Jan 2, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Jan 2, 2025Jan 2, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Jan 1, 2025Jan 1, 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•17•0•0•Updated Dec 31, 2024Dec 31, 2024
IMPA
Public
Jupyter Notebook
•0•9•1•0•Updated Dec 31, 2024Dec 31, 2024
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 Dec 26, 2024Dec 26, 2024
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•3•0•Updated Dec 26, 2024Dec 26, 2024
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•6•16•5•2•Updated Dec 23, 2024Dec 23, 2024
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•34•2•1•Updated Dec 23, 2024Dec 23, 2024
ehrdata
Public
A datastructure for EHR data
Python
•
Apache License 2.0
•1•5•16•3•Updated Dec 23, 2024Dec 23, 2024
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
•21•249•41•4•Updated Dec 23, 2024Dec 23, 2024
prophet
Public
Python
•
MIT License
•2•27•2•0•Updated Dec 22, 2024Dec 22, 2024
single-cell-transformer-papers
Public
HTML
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Other
•36•287•39•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•321•34•6•Updated Dec 20, 2024Dec 20, 2024
neural_organoid_atlas
Public
Reproducibility repository for the Human Neural Organoid Atlas publication
Jupyter Notebook
•4•25•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
•
BSD 3-Clause "New" or "Revised" License
•47•355•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
pertpy-reproducibility
Public
Jupyter Notebook
•
Apache License 2.0
•1•1•0•0•Updated Dec 9, 2024Dec 9, 2024
scvelo
Public
RNA Velocity generalized through dynamical modeling
Python
•
BSD 3-Clause "New" or "Revised" License
•104•421•56•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
•
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•7•0•0•Updated Dec 1, 2024Dec 1, 2024
spapros
Public
Python package for Probe set selection for targeted spatial transcriptomics.
Python
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MIT License
•7•33•3•9•Updated Nov 29, 2024Nov 29, 2024
atlas-feature-selection-benchmark
Public
Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying"
benchmarking integration feature-selection scrna-seq
Jupyter Notebook
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MIT License
•0•5•0•0•Updated Nov 25, 2024Nov 25, 2024