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

rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

bonesistools

Python package providing bioinformatics tools for upstream and downstream analysis of the BoNesis framework

cytetype

Python client for characterization of clusters from single-cell RNA-seq data.

annsql

The AnnSQL package enables SQL based queries on AnnData objects.

torch-adata

Create PyTorch Datasets from AnnData

scxpand

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

drvi-py

Unsupervised Deep Disentangled Representation of Single-Cell Omics

treedata

anndata with trees

scxpand-cuda

Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing (CUDA-enabled)

geome

Geometric Learning for Genome Data

grnndata

Awesome GRN enhanced AnnData toolkit

pytximport

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

vintools

Michael Vinyard's utilities

mudatasets

Multimodal datasets, in MuData format

pylimma

Python port of R limma for differential expression analysis