scverse

Foundational tools for omics data in the life sciences

Pinned Repositories

anndata
Annotated data.
Language:Python563 14 718152
mudata
Multimodal Data (.h5mu) implementation for Python
Language:Python73 6 5217
muon
muon is a multimodal omics Python framework
Language:Python209 14 10730
rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
Language:Python139 9 5419
scanpy
Single-cell analysis in Python. Scales to >1M cells.
Language:Python1.9k 51 1.7k594
scanpy-tutorials
Scanpy Tutorials.
Language:Jupyter Notebook182 10 45112
scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Language:Python214 10 28834
scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language:Python1.2k 25 1k344
spatialdata
An open and interoperable data framework for spatial omics data
Language:Python218 10 36542
squidpy
Spatial Single Cell Analysis in Python
Language:Python424 9 50078

scverse's Repositories

scverse/scanpy
Single-cell analysis in Python. Scales to >1M cells.
Language:Python1.9k 51 1.7k594
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language:Python1.2k 25 1k344
scverse/anndata
Annotated data.
Language:Python563 14 718152
scverse/squidpy
Spatial Single Cell Analysis in Python
Language:Python424 9 50078
scverse/spatialdata
An open and interoperable data framework for spatial omics data
Language:Python218 10 36542
scverse/scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Language:Python214 10 28834
scverse/scanpy-tutorials
Scanpy Tutorials.
Language:Jupyter Notebook182 10 45112
scverse/rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
Language:Python139 9 5419
scverse/pertpy
Perturbation Analysis in the scverse ecosystem.
Language:Python126 5 23520
scverse/mudata
Multimodal Data (.h5mu) implementation for Python
Language:Python73 6 5217
scverse/cookiecutter-scverse
Cookiecutter template for scverse
Language:Python67 5 858
scverse/anndataR
AnnData interoperability in R
Language:R53 9 678
scverse/scvi-tutorials
Notebooks used in scvi-tools tutorials
Language:Jupyter Notebook44 6 4824
scverse/pytometry
Flow & mass cytometry analytics.
Language:Python41 4 2710
scverse/napari-spatialdata
Interactive visualization of spatial omics data
Language:Python36 12 12315
scverse/spatialdata-io
Language:Python36 5 8324
scverse/spatialdata-notebooks
Language:Jupyter Notebook35 2 2117
scverse/squidpy_notebooks
Tutorials for Squidpy
Language:Jupyter Notebook28 3 3417
scverse/spatialdata-plot
Static plotting for spatialdata
Language:Python27 7 14913
scverse/genomic-features
Genomic Features in Python from BioConductor's AnnotationHub
Language:Python19 3 335
scverse/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Language:Python18 5 1540
scverse/anndata-tutorials
Use cases for anndata.
Language:Jupyter Notebook13 6 312
scverse/scverse-tutorials
Tutorials for learning scverse
Language:Python11 6 3112
scverse/conference-2024
Slides and Notebooks for scverse 2024
Language:Jupyter Notebook92
scverse/governance
Governance docs for scverse
6 7 50
scverse/pertpy-tutorials
Language:Jupyter Notebook4 4 99
scverse/cookiecutter-scverse-instance
Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.
Language:Python1 1 02
scverse/plotting_api
Experimenting with a simplified plotting API for scanpy/scirpy
Language:Jupyter Notebook1 2 3
scverse/cookiecutter-scverse-presentation
Introduction to our template
scverse/prelude-runner
Jupyter notebook runner that executes preludes before each cell
Language:Python3 1