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

adpbulk

pseudobulking on an AnnData object

rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

bonesistools

Python-implemented toolkits for upstream and downstream analyses around the BoNesis ecosystem.

cirrocumulus

Bring your single-cell data to life

rapids-singlecell-cu13

rapids-singlecell: GPU-accelerated framework for scRNA analysis

rapids-singlecell-cu12

rapids-singlecell: GPU-accelerated framework for scRNA analysis

drvi-py

Unsupervised Deep Disentangled Representation of Single-Cell Omics

cytetype

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

scxpand

Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing

annsql

A Python SQL tool for converting Anndata objects to a relational DuckDb database. Methods are included for querying and basic single-cell preprocessing (experimental).

scxpand-cuda

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

treedata

anndata with trees

torch-adata

Create PyTorch Datasets from AnnData

grnndata

Awesome GRN enhanced AnnData toolkit

mudatasets

Multimodal datasets, in MuData format

pytximport

pytximport is Python implementation of `tximport` to transform transcript counts from transcriptome mapping tools into gene count estimations.

metaspace-converter

Convert Metaspace datasets to AnnData

cellplots

Plotting assistant and resources

vintools

Michael Vinyard's utilities