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232 repositories

hadge
Public
Comprehensive pipeline for donor demultiplexing in single cell
single-cell deconvolution demultiplexing
Nextflow
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MIT License
•8•24•11•1•Updated Jun 14, 2025Jun 14, 2025
regvelo
Public
inferring regulatory cellular dynamics
generative-model rna-velocity-estimation perturbation-analysis grn-inference single-cell-dynamics
Python
•
BSD 3-Clause "New" or "Revised" License
•3•44•3•0•Updated Jun 14, 2025Jun 14, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•5•0•0•Updated Jun 14, 2025Jun 14, 2025
ehrapy-datasets
Public
A collection of scripts to generate AnnData objects of EHR datasets for ehrapy
Jupyter Notebook
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Apache License 2.0
•2•7•3•0•Updated Jun 13, 2025Jun 13, 2025
CellFlow
Public
Modeling complex perturbations with CellFlow
Python
•
Other
•6•51•46•11•Updated Jun 13, 2025Jun 13, 2025
ehrdata
Public
A datastructure for EHR data
data-analysis ehr ehrapy
Python
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Apache License 2.0
•1•5•18•1•Updated Jun 12, 2025Jun 12, 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
•26•293•42•2•Updated Jun 12, 2025Jun 12, 2025
archmap
Public
JavaScript
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MIT License
•0•4•3•0•Updated Jun 11, 2025Jun 11, 2025
mapqc
Public
MapQC - a metric for the evaluation of single-cell query-to-reference mappings
integration mapping transcriptomics single-cell atlas query-to-reference-mapping
Python
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MIT License
•1•8•0•0•Updated Jun 11, 2025Jun 11, 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•44•7•3•Updated Jun 10, 2025Jun 10, 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
•19•134•14•1•Updated Jun 10, 2025Jun 10, 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 Jun 10, 2025Jun 10, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
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BSD 3-Clause "New" or "Revised" License
•7•26•4•2•Updated Jun 9, 2025Jun 9, 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
•10•163•34•6•Updated Jun 9, 2025Jun 9, 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 Jun 9, 2025Jun 9, 2025
spatialdata-db
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•1•4•26•3•Updated Jun 9, 2025Jun 9, 2025
devVI
Public
Integration of developmental scRNA-seq data
Python
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MIT License
•1•0•0•1•Updated Jun 9, 2025Jun 9, 2025
zellkonverter
Public
Conversion between scRNA-seq objects
r conversion scrna-seq bioconductor
R
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Other
•29•175•12•1•Updated Jun 8, 2025Jun 8, 2025
idtrack
Public
Cross-Temporal and Cross-Database Biological Identifier Mapping
Python
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BSD 3-Clause "New" or "Revised" License
•0•1•1•0•Updated Jun 8, 2025Jun 8, 2025
archmap_data
Public
Python
•0•1•1•1•Updated Jun 6, 2025Jun 6, 2025
multimil
Public
Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
Python
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BSD 3-Clause "New" or "Revised" License
•6•33•9•1•Updated Jun 3, 2025Jun 3, 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•4•Updated Jun 2, 2025Jun 2, 2025
scProtVelo
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jun 2, 2025Jun 2, 2025
regvelo_reproducibility
Public
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•8•0•1•Updated Jun 2, 2025Jun 2, 2025
single-cell-best-practices
Public
https://www.sc-best-practices.org
tutorial rna-seq book single-cell
Jupyter Notebook
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Other
•218•923•68•3•Updated May 31, 2025May 31, 2025
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
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Apache License 2.0
•2•9•1•0•Updated May 23, 2025May 23, 2025
single-cell-transformer-papers
Public
HTML
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Other
•41•319•40•0•Updated May 23, 2025May 23, 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
•60•369•53•8•Updated May 22, 2025May 22, 2025
DRVI_tutorials
Public
All the official tutorials for DRVI
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated May 21, 2025May 21, 2025
txsim
Public
Python
•1•3•36•4•Updated May 12, 2025May 12, 2025

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