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

Annotated data.

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

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

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial data in an easy and efficient way.

muon is a multimodal omics Python framework

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

Scanpy Tutorials.

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

Episcanpy: Epigenomics Single Cell Analysis in Python

Convert between AnnData and SingleCellExperiment

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

Learning cell communication from spatial graphs of cells

Gene group activity utility functions for Scanpy

Bring your single-cell data to life

Scanpy use cases.

BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.

Scripts for using scanpy

pseudobulking on an AnnData object

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

🧬 Analyze spatial transcriptomics data through natural language conversation. Stop writing code, start having conversations with your data. MCP server for Claude Code and Codex.

A collection of project templates and useful functions for single-cell data analysis with Scanpy.

SCeptre is a python package that extends the functionalities of Scanpy to analyze multiplexed single-cell proteomics data.

Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark

A guide to using the Python scRNA-seq analysis package Scanpy from R

Fast spatial deconvolution via leverage-score sketching — scales to million-spot datasets while preserving rare cell type signals.

Collection of Sphinx extensions similar to (but more flexible than) numpydoc

Add images to StereoSeq/Stomics spatial data and generate an RDS(Seurat) and h5ad (Scanpy).