scverse

Single-cell analysis in Python. Scales to >100M cells.

Deep probabilistic analysis of single-cell and spatial omics data

🧬 gget enables efficient querying of genomic reference databases

Annotated data.

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Spatial Single Cell Analysis in Python

CellRank: dynamics from multi-view single-cell data

rapids-singlecell: GPU-accelerated framework for scRNA analysis

An open and interoperable data framework for spatial omics data

Single-cell perturbation analysis

Single-cell epigenomics analysis tools

LIANA+: an all-in-one framework for cell-cell communication

Python package to perform enrichment analysis from omics data.

muon is a multimodal omics Python framework

A scanpy extension to analyse single-cell TCR and BCR data.

Scanpy Tutorials.

AnnData interoperability in R

Multimodal Data (.h5mu) implementation for Python

A rust implementation of STAR

Interactive visualization of spatial omics data

Cookiecutter template for scverse

Static plotting for spatialdata

Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

Notebooks used in scvi-tools tutorials

Flow & mass cytometry analytics.