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273 repositories

gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•8•1•0•Updated Aug 10, 2026Aug 10, 2026
rapids-singlecell-reproducibility
Public
Jupyter Notebook
•
MIT License
•0•1•0•1•Updated Aug 10, 2026Aug 10, 2026
sckitflow
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•7•25•7•Updated Aug 10, 2026Aug 10, 2026
single-cell-best-practices
Public
https://www.sc-best-practices.org
tutorial rna-seq book
tutorial rna-seq book single-cell
Jupyter Notebook
•
Other
•277•1.2k•58•4•Updated Aug 10, 2026Aug 10, 2026
cellink
Public
Scalable framework for integrating single-cell omics with genetic data using AnnData.
genetics single-cell anndata
genetics single-cell anndata
Python
•
Apache License 2.0
•5•20•6•1•Updated Aug 10, 2026Aug 10, 2026
embpy
Public
Python
•
MIT License
•1•20•9•2•Updated Aug 10, 2026Aug 10, 2026
geome
Public
microscopy graph-learning pytorch-geometric
microscopy graph-learning pytorch-geometric anndata
Python
•
MIT License
•4•17•7•1•Updated Aug 9, 2026Aug 9, 2026
squidpy-ports
Public
Reference implementations and fixture generators for squidpy ports
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Aug 7, 2026Aug 7, 2026
interscale
Public
InterScale: multi-scale cellular interaction analysis model for spatial transcriptomics
spatial-transcriptomics graph-transformer cell-cell-communication
spatial-transcriptomics graph-transformer cell-cell-communication
Python
•
BSD 3-Clause "New" or "Revised" License
•1•11•8•4•Updated Aug 7, 2026Aug 7, 2026
scfit
Public
Python
•
MIT License
•0•2•1•1•Updated Aug 7, 2026Aug 7, 2026
ehrdata
Public
A datastructure for EHR data
data-analysis ehr ehrapy
data-analysis ehr ehrapy
Python
•
Apache License 2.0
•6•15•11•3•Updated Aug 7, 2026Aug 7, 2026
ehrapy
Public
Electronic Health Record Analysis with Python.
ehr electronic-health-record scverse
ehr electronic-health-record scverse electronic-medical-record
Python
•
Apache License 2.0
•50•360•15•6•Updated Aug 6, 2026Aug 6, 2026
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
•
Apache License 2.0
•2•9•0•1•Updated Aug 6, 2026Aug 6, 2026
nbconvertR
Public
Vignette Engine wrapping Jupyter Notebooks
R
•2•3•0•1•Updated Aug 6, 2026Aug 6, 2026
ReconEval
Public
Benchmarking for gene expression from single cell latent representations
Jupyter Notebook
•
MIT License
•2•20•1•0•Updated Aug 5, 2026Aug 5, 2026
scConcept
Public
Contrastive pre-training for technology-agnostic single-cell representations beyond reconstruction
transcriptomics single-cell contrastive-learning
transcriptomics single-cell contrastive-learning foundation-models
Python
•
MIT License
•7•38•2•1•Updated Aug 4, 2026Aug 4, 2026
cellucid
Public
See every cell. Query any gene. Fly through millions. Zero friction.
JavaScript
•
BSD 3-Clause "New" or "Revised" License
•0•5•0•0•Updated Aug 4, 2026Aug 4, 2026
regvelo
Public
inferring regulatory cellular dynamics
generative-model rna-velocity-estimation perturbation-analysis
generative-model rna-velocity-estimation perturbation-analysis grn-inference single-cell-dynamics
Python
•
BSD 3-Clause "New" or "Revised" License
•18•181•1•1•Updated Aug 4, 2026Aug 4, 2026
cellucid-python
Public
The complete Python toolkit for Cellucid. Serve, export, document, explore.
Python
•
BSD 3-Clause "New" or "Revised" License
•0•3•0•0•Updated Aug 4, 2026Aug 4, 2026
cellucid-datasets
Public
Sample dataset exports for the Cellucid web app, hosted separately to keep the app lightweight and allow independent dataset updates.
Jupyter Notebook
•
Other
•0•0•0•0•Updated Aug 4, 2026Aug 4, 2026
anndata2ri
Public
Convert between AnnData and SingleCellExperiment
jupyter bioconductor single-cell
jupyter bioconductor single-cell rpy2 scanpy
Python
•
GNU General Public License v3.0
•19•152•11•0•Updated Aug 4, 2026Aug 4, 2026
scanpydoc
Public
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
Python
•
GNU General Public License v3.0
•5•12•4•0•Updated Aug 4, 2026Aug 4, 2026
chem-perturbridge_lpm
Public
Python
•
MIT License
•0•0•0•0•Updated Aug 3, 2026Aug 3, 2026
spatialdata-db
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•1•12•26•3•Updated Aug 3, 2026Aug 3, 2026
moscot
Public
Multi-omic single-cell optimal transport tools
single-cell optimal-transport
single-cell optimal-transport
Python
•
BSD 3-Clause "New" or "Revised" License
•16•214•31•5•Updated Aug 3, 2026Aug 3, 2026
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
•
BSD 3-Clause "New" or "Revised" License
•8•34•2•2•Updated Aug 3, 2026Aug 3, 2026
troutpy
Public
Package for the analysis of Transcripts outside segmented cells in ST data
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•2•31•0•2•Updated Aug 3, 2026Aug 3, 2026
mapqc
Public
MapQC - a metric for the evaluation of single-cell query-to-reference mappings
integration mapping transcriptomics
integration mapping transcriptomics single-cell atlas query-to-reference-mapping
Python
•
MIT License
•1•12•0•2•Updated Aug 3, 2026Aug 3, 2026
CellFlow
Public
Modeling complex perturbations with CellFlow
Python
•
MIT License
•27•153•50•18•Updated Aug 3, 2026Aug 3, 2026
DRVI
Public
Unsupervised Deep Disentangled Representation of Single-Cell Omics
python bioinformatics integration
python bioinformatics integration transcriptomics single-cell disentanglement anndata
Python
•
BSD 3-Clause "New" or "Revised" License
•5•72•5•3•Updated Aug 3, 2026Aug 3, 2026

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273 repositories

gh-dashboard

rapids-singlecell-reproducibility

sckitflow

single-cell-best-practices

cellink

embpy

geome

squidpy-ports

interscale

scfit

ehrdata

ehrapy

ehrapy-tutorials

nbconvertR

ReconEval

scConcept

cellucid

regvelo

cellucid-python

cellucid-datasets

anndata2ri

scanpydoc

chem-perturbridge_lpm

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multigrate

troutpy

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273 repositories