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

Annotated data.

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

muon is a multimodal omics Python framework

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

A guide to using a Seurat object in conjunction with RNA Velocity

SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.

Multimodal Data (.h5mu) implementation for Python

Bring your single-cell data to life

AnnData interoperability in R

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Feature-rich Python implementation of the tximport package for gene count estimation.

pseudobulking on an AnnData object

.h5mu files interface for Seurat

Muon for Julia

The AnnSQL package enables SQL based queries on AnnData objects.

Create PyTorch Datasets from AnnData

Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.