Projects in Awesome Lists tagged with scverse
A curated list of projects in awesome lists tagged with 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/rapids-singlecell
rapids-singlecell: GPU-accelerated framework for scRNA analysis
anndata bioinformatics gpu scverse single-cell
Last synced: 01 Apr 2026
https://github.com/theislab/ehrapy
Electronic Health Record Analysis with Python.
ehr electronic-health-record electronic-medical-record scverse
Last synced: 11 Oct 2025
https://github.com/scverse/pertpy
Single-cell perturbation analysis
perturbation scverse single-cell
Last synced: 02 Apr 2026
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/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/scvi-tutorials
Notebooks used in scvi-tools tutorials
Last synced: 07 Jul 2025
https://github.com/complextissue/pytximport
Feature-rich Python implementation of the tximport package for gene count estimation.
anndata bioinformatics deseq2 python rna rna-seq scverse tximport
Last synced: 25 Feb 2026
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/biocontext-ai/knowledgebase-mcp
BioContextAI Knowledgebase MCP server for biomedical agentic AI
agentic-ai biomedical-ai llm mcp mcp-server model-context-protocol scverse
Last synced: 28 Feb 2026
https://github.com/complextissue/spatiomic
A Python package for unsupervised analysis of spatial (prote)omics data.
image-analysis multiplexed-imaging pathology pathoplex scverse spatial-proteomics spatial-statistics
Last synced: 05 Mar 2026
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/complextissue/pyclustree
A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.
clustree pyclustree scverse single-cell
Last synced: 25 Feb 2026
https://github.com/tiledb-inc/scverse-ml-workshop-2024
Scripts/Notebooks for "Training models on atlas-scale single-cell datasets" at scverse Conference 2024
scverse single-cell single-cell-rna-seq tiledb
Last synced: 10 Apr 2025
https://github.com/vjcitn/scvir
experimental interface between R and scvi-tools
Last synced: 28 Apr 2025
https://github.com/gtca/chame
Chromatin analysis module
atac-seq chromatin genome multiome ranges scatac-seq scverse
Last synced: 01 Sep 2025
