scverse

Foundational tools for omics data in the life sciences

Pinned Repositories

anndata
Annotated data.
Language:Python683 13 824177
decoupler
Python package to perform enrichment analysis from omics data.
Language:Python237 4 18635
muon
muon is a multimodal omics Python framework
Language:Python253 10 12031
rapids_singlecell
rapids_singlecell: GPU-accelerated framework for scRNA analysis
Language:Python260 9 10535
scanpy
Single-cell analysis in Python. Scales to >100M cells.
Language:Python2.3k 47 1.9k678
scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Language:Python242 9 32341
scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language:Python1.5k 26 1.1k418
SnapATAC2
Single-cell epigenomics analysis tools
Language:Python298 8 34935
spatialdata
An open and interoperable data framework for spatial omics data
Language:Python322 13 52273
squidpy
Spatial Single Cell Analysis in Python
Language:Python529 10 58998

scverse's Repositories

scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
Language:Python2.3k 47 1.9k678
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language:Python1.5k 26 1.1k418
scverse/anndata
Annotated data.
Language:Python683 13 824177
scverse/squidpy
Spatial Single Cell Analysis in Python
Language:Python529 10 58998
scverse/spatialdata
An open and interoperable data framework for spatial omics data
Language:Python322 13 52273
scverse/rapids_singlecell
rapids_singlecell: GPU-accelerated framework for scRNA analysis
Language:Python260 9 10535
scverse/scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Language:Python242 9 32341
scverse/scanpy-tutorials
Scanpy Tutorials.
Language:Jupyter Notebook228 9 49120
scverse/pertpy
Single-cell perturbation analysis
Language:Python212 5 33235
scverse/anndataR
AnnData interoperability in R
Language:R121 10 8514
scverse/cookiecutter-scverse
Cookiecutter template for scverse
Language:Python84 5 11914
scverse/spatialdata-io
Language:Python75 7 14449
scverse/napari-spatialdata
Interactive visualization of spatial omics data
Language:Python71 12 15621
scverse/spatialdata-plot
Static plotting for spatialdata
Language:Python68 7 24418
scverse/spatialdata-notebooks
Language:Jupyter Notebook62 2 2626
scverse/scvi-tutorials
Notebooks used in scvi-tools tutorials
Language:Jupyter Notebook57 5 6030
scverse/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Language:Python30 6 1759
scverse/genomic-features
Genomic Features in Python from BioConductor's AnnotationHub
Language:Python22 3 335
scverse/scverse-tutorials
Tutorials for learning scverse
Language:Python18 7 3415
scverse/fast-array-utils
Fast array utilities
Language:Python121
scverse/pertpy-tutorials
Language:Jupyter Notebook11 3 89
scverse/anndata-plot
Language:Python9 3 13
scverse/session-info2
Language:Python7 1 121
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:Python5 0 04
scverse/cookiecutter-scverse-presentation
Introduction to our template
2 2 0
scverse/plotting_api
Experimenting with a simplified plotting API for scanpy/scirpy
Language:Jupyter Notebook2 1 4
scverse/scvi-colab
Lightweight helper to install scvi-tools in Google Colab
Language:Python2 6 31
scverse/prelude-runner
Jupyter notebook runner that executes preludes before each cell
Language:Python1 2 1
scverse/scvi-tools-site
Language:JavaScript1 5 02
scverse/zulip-bots
Repository for zulip bots for scverse.zulipchat.com
2 0