Theis Lab

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214 repositories

gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Dec 28, 2024Dec 28, 2024
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Dec 27, 2024Dec 27, 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
IMPA
Public
Jupyter Notebook
•0•9•1•0•Updated Dec 26, 2024Dec 26, 2024
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•15•1•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
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 Dec 23, 2024Dec 23, 2024
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•119•31•4•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
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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
•20•245•41•4•Updated Dec 23, 2024Dec 23, 2024
prophet
Public
Python
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MIT License
•2•27•2•0•Updated Dec 22, 2024Dec 22, 2024
single-cell-transformer-papers
Public
HTML
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Other
•35•285•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
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BSD 3-Clause "New" or "Revised" License
•47•355•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•155•12•1•Updated Dec 10, 2024Dec 10, 2024
pertpy-reproducibility
Public
Jupyter Notebook
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Apache License 2.0
•1•1•0•0•Updated Dec 9, 2024Dec 9, 2024
scvelo
Public
RNA Velocity generalized through dynamical modeling
Python
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BSD 3-Clause "New" or "Revised" License
•104•421•56•2•Updated Dec 9, 2024Dec 9, 2024
archmap_data
Public
Python
•0•1•1•1•Updated Dec 6, 2024Dec 6, 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•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•32•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
spapros-pipeline
Public
Nextflow
•0•7•0•0•Updated Nov 23, 2024Nov 23, 2024