Theis Lab

All

210 repositories

anndata2ri
Public
Convert between AnnData and SingleCellExperiment
jupyter bioconductor single-cell rpy2 scanpy
Python
•
GNU General Public License v3.0
•16•128•13•0•Updated Oct 30, 2024Oct 30, 2024
scanpydoc
Public
Collection of Sphinx extensions similar to (but more flexible than) numpydoc
Python
•
GNU General Public License v3.0
•6•12•3•0•Updated Oct 30, 2024Oct 30, 2024
archmap_data
Public
Python
•0•1•1•1•Updated Oct 30, 2024Oct 30, 2024
moscot
Public
Multi-omic single-cell optimal transport tools
single-cell optimal-transport
Python
•
BSD 3-Clause "New" or "Revised" License
•9•112•37•4•Updated Oct 30, 2024Oct 30, 2024
ehrdata
Public
A datastructure for EHR data
Python
•
Apache License 2.0
•1•5•18•3•Updated Oct 29, 2024Oct 29, 2024
neural_organoid_atlas
Public
Reproducibility repository for the Human Neural Organoid Atlas publication
Jupyter Notebook
•1•14•2•0•Updated Oct 29, 2024Oct 29, 2024
gh-dashboard
Public
A dashboard of everything in the theislab GitHub repository
HTML
•0•2•0•0•Updated Oct 29, 2024Oct 29, 2024
archmap
Public
JavaScript
•
MIT License
•0•4•2•0•Updated Oct 29, 2024Oct 29, 2024
ehrapy
Public
Electronic Health Record Analysis with Python.
ehr electronic-health-record scverse electronic-medical-record
Python
•
Apache License 2.0
•20•222•43•3•Updated Oct 29, 2024Oct 29, 2024
multigrate
Public
Multigrate: multiomic data integration for single-cell genomics
Python
•
BSD 3-Clause "New" or "Revised" License
•6•15•5•2•Updated Oct 28, 2024Oct 28, 2024
pertpy-reproducibility
Public
Jupyter Notebook
•
Apache License 2.0
•0•0•0•0•Updated Oct 28, 2024Oct 28, 2024
destiny
Public
R package for single cell and other data analysis using diffusion maps
r dimensionality-reduction diffusion-maps
R
•
GNU General Public License v3.0
•11•76•32•0•Updated Oct 28, 2024Oct 28, 2024
ehrapy-tutorials
Public
Tutorials for ehrapy
Jupyter Notebook
•
Apache License 2.0
•2•7•0•0•Updated Oct 28, 2024Oct 28, 2024
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
•51•335•42•7•Updated Oct 27, 2024Oct 27, 2024
IMPA
Public
Jupyter Notebook
•0•9•0•0•Updated Oct 27, 2024Oct 27, 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
•
MIT License
•0•5•0•0•Updated Oct 26, 2024Oct 26, 2024
single-cell-best-practices
Public
https://www.sc-best-practices.org
tutorial rna-seq book single-cell
Jupyter Notebook
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Other
•181•765•66•3•Updated Oct 25, 2024Oct 25, 2024
spapros
Public
Python package for Probe set selection for targeted spatial transcriptomics.
Python
•
MIT License
•6•23•3•10•Updated Oct 21, 2024Oct 21, 2024
CFGen
Public
Python
•
MIT License
•4•6•2•0•Updated Oct 21, 2024Oct 21, 2024
zellkonverter
Public
Conversion between scRNA-seq objects
r conversion scrna-seq bioconductor
R
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Other
•27•149•11•1•Updated Oct 21, 2024Oct 21, 2024
cross_system_integration
Public
Jupyter Notebook
•2•10•11•0•Updated Oct 19, 2024Oct 19, 2024
single-cell-transformer-papers
Public
Other
•28•236•24•0•Updated Oct 18, 2024Oct 18, 2024
multimil
Public
Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
Python
•
BSD 3-Clause "New" or "Revised" License
•3•18•4•0•Updated Oct 16, 2024Oct 16, 2024
spatialdata-db
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•1•25•0•Updated Oct 16, 2024Oct 16, 2024
archmap_doc
Public
Python
•0•0•0•0•Updated Oct 16, 2024Oct 16, 2024
task-dge-perturbation-prediction-analysis
Public
Jupyter Notebook
•
MIT License
•0•3•0•0•Updated Oct 15, 2024Oct 15, 2024
moscot_notebooks
Public
Analysis notebooks using the moscot package
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•3•7•2•3•Updated Oct 8, 2024Oct 8, 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
•
BSD 3-Clause "New" or "Revised" License
•46•346•19•0•Updated Oct 7, 2024Oct 7, 2024
moslin
Public
Code, data and analysis for moslin.
genomics reproducible-research tracing transport optimal cell lineage single
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•1•11•0•0•Updated Oct 7, 2024Oct 7, 2024
txsim
Public
Python
•0•3•36•4•Updated Oct 3, 2024Oct 3, 2024