Theis Lab

All

221 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
•204•856•70•3•Updated Mar 9, 2025Mar 9, 2025
scaling_flow
Public
CellFlow across datasets, à la Prophet
Python
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Other
•2•0•0•0•Updated Mar 9, 2025Mar 9, 2025
cell_flow_perturbation
Public
Modeling complex perturbations with CellFlow
Python
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Other
•2•4•36•11•Updated Mar 9, 2025Mar 9, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Mar 9, 2025Mar 9, 2025
zellkonverter
Public
Conversion between scRNA-seq objects
r conversion scrna-seq bioconductor
R
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Other
•28•159•12•2•Updated Mar 9, 2025Mar 9, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Mar 8, 2025Mar 8, 2025
mapqc
Public
Python
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MIT License
•0•0•0•0•Updated Mar 7, 2025Mar 7, 2025
vevo_Tahoe_100m_analysis
Public
Jupyter Notebook
•1•9•0•1•Updated Mar 7, 2025Mar 7, 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
•23•276•44•2•Updated Mar 7, 2025Mar 7, 2025
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
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Apache License 2.0
•2•9•0•1•Updated Mar 7, 2025Mar 7, 2025
devVI
Public
Integration of developmental scRNA-seq data
Python
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MIT License
•0•0•0•0•Updated Mar 7, 2025Mar 7, 2025
ehrdata
Public
A datastructure for EHR data
Python
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Apache License 2.0
•1•5•20•1•Updated Mar 7, 2025Mar 7, 2025
single-cell-transformer-papers
Public
HTML
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Other
•37•301•40•0•Updated Mar 6, 2025Mar 6, 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•140•36•4•Updated Mar 6, 2025Mar 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 Mar 5, 2025Mar 5, 2025
pertpy-reproducibility
Public
Jupyter Notebook
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Apache License 2.0
•1•3•0•0•Updated Mar 5, 2025Mar 5, 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 Mar 5, 2025Mar 5, 2025
spatialdata-db
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•25•2•Updated Mar 4, 2025Mar 4, 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 Mar 4, 2025Mar 4, 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
•18•132•13•0•Updated Mar 4, 2025Mar 4, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•6•20•4•2•Updated Mar 3, 2025Mar 3, 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•38•3•1•Updated Mar 3, 2025Mar 3, 2025
cross_system_integration
Public
Jupyter Notebook
•2•11•11•0•Updated Mar 2, 2025Mar 2, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Mar 1, 2025Mar 1, 2025
archmap_doc
Public
Python
•0•0•0•0•Updated Feb 26, 2025Feb 26, 2025
diffxpy
Public
Differential expression analysis for single-cell RNA-seq data.
bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq
Python
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BSD 3-Clause "New" or "Revised" License
•23•196•102•6•Updated Feb 25, 2025Feb 25, 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
•53•354•49•7•Updated Feb 25, 2025Feb 25, 2025
CFGen
Public
Python
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MIT License
•4•7•0•0•Updated Feb 25, 2025Feb 25, 2025
prophet
Public
Python
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MIT License
•2•29•0•0•Updated Feb 25, 2025Feb 25, 2025
scvelo
Public
RNA Velocity generalized through dynamical modeling
Python
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BSD 3-Clause "New" or "Revised" License
•105•431•60•3•Updated Feb 24, 2025Feb 24, 2025