Theis Lab

All

218 repositories

cell_flow_perturbation
Public
Modeling complex perturbations with CellFlow
Python
•
Other
•1•4•34•10•Updated Mar 2, 2025Mar 2, 2025
single-cell-best-practices
Public
https://www.sc-best-practices.org
tutorial rna-seq book single-cell
Jupyter Notebook
•
Other
•201•854•71•4•Updated Mar 2, 2025Mar 2, 2025
pertpy-reproducibility
Public
Jupyter Notebook
•
Apache License 2.0
•1•3•0•0•Updated Mar 2, 2025Mar 2, 2025
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•3•0•0•Updated Mar 2, 2025Mar 2, 2025
devVI
Public
Integration of developmental scRNA-seq data
Python
•
MIT License
•0•0•0•0•Updated Mar 2, 2025Mar 2, 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
ehrapy
Public
Electronic Health Record Analysis with Python.
ehr electronic-health-record scverse electronic-medical-record
Python
•
Apache License 2.0
•22•269•43•1•Updated Feb 27, 2025Feb 27, 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
•
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
•
BSD 3-Clause "New" or "Revised" License
•53•352•49•7•Updated Feb 25, 2025Feb 25, 2025
CFGen
Public
Python
•
MIT License
•4•6•0•0•Updated Feb 25, 2025Feb 25, 2025
prophet
Public
Python
•
MIT License
•2•29•0•0•Updated Feb 25, 2025Feb 25, 2025
scanpydoc
Public
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
Python
•
GNU General Public License v3.0
•6•12•2•0•Updated Feb 25, 2025Feb 25, 2025
zellkonverter
Public
Conversion between scRNA-seq objects
r conversion scrna-seq bioconductor
R
•
Other
•28•159•13•2•Updated Feb 25, 2025Feb 25, 2025
anndata2ri
Public
Convert between AnnData and SingleCellExperiment
jupyter bioconductor single-cell rpy2 scanpy
Python
•
GNU General Public License v3.0
•18•132•13•0•Updated Feb 24, 2025Feb 24, 2025
moscot
Public
Multi-omic single-cell optimal transport tools
single-cell optimal-transport
Python
•
BSD 3-Clause "New" or "Revised" License
•9•136•35•5•Updated Feb 24, 2025Feb 24, 2025
spatialdata-db
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•1•25•2•Updated Feb 24, 2025Feb 24, 2025
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
•
BSD 3-Clause "New" or "Revised" License
•6•20•4•2•Updated Feb 24, 2025Feb 24, 2025
DRVI
Public
Unsupervised Deep Disentangled Representation of Single-Cell Omics
python bioinformatics integration transcriptomics single-cell disentanglement anndata
Python
•
BSD 3-Clause "New" or "Revised" License
•3•38•3•1•Updated Feb 24, 2025Feb 24, 2025
ehrdata
Public
A datastructure for EHR data
Python
•
Apache License 2.0
•1•5•19•2•Updated Feb 24, 2025Feb 24, 2025
scvelo
Public
RNA Velocity generalized through dynamical modeling
Python
•
BSD 3-Clause "New" or "Revised" License
•105•430•60•3•Updated Feb 24, 2025Feb 24, 2025
archmap
Public
JavaScript
•
MIT License
•0•4•3•0•Updated Feb 18, 2025Feb 18, 2025
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
•
Apache License 2.0
•2•9•0•0•Updated Feb 17, 2025Feb 17, 2025
deconvATAC
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•1•Updated Feb 17, 2025Feb 17, 2025
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
•48•370•19•0•Updated Feb 17, 2025Feb 17, 2025
single-cell-transformer-papers
Public
HTML
•
Other
•38•300•40•1•Updated Feb 14, 2025Feb 14, 2025
inVAE_reproducibility
Public
Jupyter Notebook
•0•0•0•0•Updated Feb 13, 2025Feb 13, 2025
jump-cpg0016-segmentation
Public
Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium
Jupyter Notebook
•
MIT License
•0•8•0•0•Updated Feb 6, 2025Feb 6, 2025
chemCPA
Public
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
genomics drug-discovery transfer-learning single-cell perturbation disentanglement
Jupyter Notebook
•
MIT License
•25•107•6•1•Updated Feb 6, 2025Feb 6, 2025