scverse

Foundational tools for omics data in the life sciences

Pinned Repositories

anndata
Annotated data.
Language:Python588 14 742156
mudata
Multimodal Data (.h5mu) implementation for Python
Language:Python79 6 5717
muon
muon is a multimodal omics Python framework
Language:Python222 14 11031
rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
Language:Python158 7 6523
scanpy
Single-cell analysis in Python. Scales to >1M cells.
Language:Python2k 49 1.8k608
scanpy-tutorials
Scanpy Tutorials.
Language:Jupyter Notebook191 10 47117
scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Language:Python222 10 29735
scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language:Python1.3k 26 1k366
spatialdata
An open and interoperable data framework for spatial omics data
Language:Python245 12 42447
squidpy
Spatial Single Cell Analysis in Python
Language:Python448 10 52784

scverse's Repositories

scverse/scanpy
Single-cell analysis in Python. Scales to >1M cells.
Language:Python2k 49 1.8k608
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language:Python1.3k 26 1k366
scverse/anndata
Annotated data.
Language:Python588 14 742156
scverse/squidpy
Spatial Single Cell Analysis in Python
Language:Python448 10 52784
scverse/spatialdata
An open and interoperable data framework for spatial omics data
Language:Python245 12 42447
scverse/muon
muon is a multimodal omics Python framework
Language:Python222 14 11031
scverse/scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Language:Python222 10 29735
scverse/scanpy-tutorials
Scanpy Tutorials.
Language:Jupyter Notebook191 10 47117
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:Python158 7 6523
scverse/pertpy
Perturbation Analysis in the scverse ecosystem.
Language:Python147 4 25522
scverse/cookiecutter-scverse
Cookiecutter template for scverse
Language:Python71 5 9410
scverse/anndataR
AnnData interoperability in R
Language:R64 11 7811
scverse/scvi-tutorials
Notebooks used in scvi-tools tutorials
Language:Jupyter Notebook47 7 5225
scverse/spatialdata-io
Language:Python45 6 10829
scverse/napari-spatialdata
Interactive visualization of spatial omics data
Language:Python42 14 13917
scverse/pytometry
Flow & mass cytometry analytics.
Language:Python42 4 299
scverse/spatialdata-notebooks
Language:Jupyter Notebook39 2 2219
scverse/spatialdata-plot
Static plotting for spatialdata
Language:Python38 8 19014
scverse/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Language:Python19 5 1540
scverse/genomic-features
Genomic Features in Python from BioConductor's AnnotationHub
Language:Python19 3 336
scverse/scverse-tutorials
Tutorials for learning scverse
Language:Python14 6 3213
scverse/formulaic-contrasts
Build contrasts for models defined with formulaic
Language:Python111
scverse/governance
Governance docs for scverse
7 7 52
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/pertpy-datasets
Datasets provided through pertpy
Language:Jupyter Notebook1 4 21
scverse/plotting_api
Experimenting with a simplified plotting API for scanpy/scirpy
Language:Jupyter Notebook1 2 4
scverse/scverse.github.io
scverse.org website
Language:SCSS1 6 446
scverse/cookiecutter-scverse-presentation
Introduction to our template
2 0
scverse/prelude-runner
Jupyter notebook runner that executes preludes before each cell
Language:Python3 1
scverse/spatialdata-basel-workshop-2024
Language:TeX1