Anndata Python Packages

anndata

Annotated data.

scanpy

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

mudata

Multimodal Data (.h5mu) implementation for Python

annsel

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

muon

muon is a multimodal omics Python framework

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

cirrocumulus

Bring your single-cell data to life

adpbulk

pseudobulking on an AnnData object

scxpand

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

cytetype

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

annsql

The AnnSQL package enables SQL based queries on AnnData objects.

scxpand-cuda

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

drvi-py

Unsupervised Deep Disentangled Representation of Single-Cell Omics

torch-adata

torch-adata: bridging AnnData-based data models to torch.

treedata

anndata with trees

grnndata

Awesome GRN enhanced AnnData toolkit

vintools

Michael Vinyard's utilities

pytximport

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

geome

Geometric Learning for Genome Data

pylimma

Python port of R limma for differential expression analysis

metaspace-converter

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

mudatasets

Multimodal datasets, in MuData format