Projects in Awesome Lists by scverse
A curated list of projects in awesome lists by scverse .
https://github.com/scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
anndata bioinformatics data-science machine-learning python scanpy scverse transcriptomics visualize-data
Last synced: 11 May 2025
https://github.com/scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
cite-seq deep-generative-model deep-learning human-cell-atlas scrna-seq scverse single-cell-genomics single-cell-rna-seq variational-autoencoder variational-bayes
Last synced: 14 Dec 2025
https://github.com/scverse/anndata
Annotated data.
anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics
Last synced: 29 Jan 2026
https://github.com/scverse/squidpy
Spatial Single Cell Analysis in Python
data-visualization image-analysis single-cell-genomics single-cell-rna-seq spatial-analysis spatial-transcriptomics squidpy
Last synced: 07 Jul 2025
https://github.com/scverse/rapids-singlecell
rapids-singlecell: GPU-accelerated framework for scRNA analysis
anndata bioinformatics gpu scverse single-cell
Last synced: 01 Apr 2026
https://github.com/scverse/pertpy
Single-cell perturbation analysis
perturbation scverse single-cell
Last synced: 02 Apr 2026
https://github.com/scverse/spatialdata
An open and interoperable data framework for spatial omics data
Last synced: 11 Feb 2026
https://github.com/scverse/snapatac2
Single-cell epigenomics analysis tools
Last synced: 07 Jul 2025
https://github.com/scverse/muon
muon is a multimodal omics Python framework
anndata cite-seq mudata multi-omics multimodal-data multimodal-omics-analysis muon scanpy scatac-seq scrna-seq scverse
Last synced: 07 Jul 2025
https://github.com/scverse/scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Last synced: 07 Jul 2025
https://github.com/scverse/rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
anndata bioinformatics gpu scverse single-cell
Last synced: 27 Feb 2026
https://github.com/scverse/mudata
Multimodal Data (.h5mu) implementation for Python
anndata data-analysis genomics mudata multi-omics multimodal-omics-analysis muon scverse
Last synced: 07 Jul 2025
https://github.com/scverse/cookiecutter-scverse
Cookiecutter template for scverse
Last synced: 07 Jul 2025
https://github.com/scverse/spatialdata-plot
Static plotting for spatialdata
Last synced: 02 Apr 2026
https://github.com/scverse/napari-spatialdata
Interactive visualization of spatial omics data
napari napari-plugin spatial-analysis spatial-omics visualization
Last synced: 07 Jul 2025
https://github.com/scverse/scvi-tutorials
Notebooks used in scvi-tools tutorials
Last synced: 07 Jul 2025
https://github.com/scverse/muon.jl
Muon for Julia
anndata julia mudata multi-omics muon omics scverse single-cell
Last synced: 12 Oct 2025
https://github.com/scverse/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Last synced: 07 Jul 2025
https://github.com/scverse/genomic-features
Genomic Features in Python from BioConductor's AnnotationHub
Last synced: 07 Jul 2025
https://github.com/scverse/scverse-tutorials
Tutorials for learning scverse
Last synced: 07 Jul 2025
https://github.com/scverse/muon-tutorials
Tutorials for multimodal omics data analysis
mudata multi-omics muon scverse single-cell
Last synced: 26 Oct 2025
https://github.com/scverse/formulaic-contrasts
Build contrasts for models defined with formulaic
Last synced: 07 Jul 2025
https://github.com/scverse/shadows
Shadow objects for AnnData and MuData (experimental)
Last synced: 07 Jul 2025
https://github.com/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.
Last synced: 07 Jul 2025
https://github.com/scverse/antibody-based-spatial-proteomics-guide
Guide for common steps in analyzing antiboy-based spatial proteomics data, part of the scverse proteomics consortium.
Last synced: 23 May 2026
https://github.com/scverse/pertpy-datasets
Datasets provided through pertpy
Last synced: 07 Jul 2025
https://github.com/scverse/multi-condition-comparisions
Functions for analyzing and visualizing multi-condition single-cell data (prototypes created at Cambridge hackathon)
Last synced: 07 Jul 2025
https://github.com/scverse/plotting_api
Experimenting with a simplified plotting API for scanpy/scirpy
Last synced: 11 Mar 2026
https://github.com/scverse/202503_hackathon_owkin
Repository to organise the shared hackathon with Owkin in Paris
Last synced: 07 Jul 2025
https://github.com/scverse/cookiecutter-scverse-presentation
Introduction to our template
Last synced: 09 Feb 2026
https://github.com/scverse/scvi-colab
Lightweight helper to install scvi-tools in Google Colab
Last synced: 09 Feb 2026
https://github.com/scverse/deres
Container and visualization for differential expression (and similar) result tables
Last synced: 25 Feb 2026
https://github.com/scverse/prelude-runner
Jupyter notebook runner that executes preludes before each cell
Last synced: 07 Jul 2025
https://github.com/scverse/pandas-uuid
Pandas ExtensionArray / ExtensionDType for UUID
Last synced: 14 Jan 2026
https://github.com/scverse/zulip-bots
Repository for zulip bots for scverse.zulipchat.com
Last synced: 05 Feb 2026
https://github.com/scverse/integration-testing
A repo for integration testing core packages against upstream core packages
Last synced: 10 Feb 2026