Scanpy Python Packages

anndata

Annotated data.

scanpy

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

muon

muon is a multimodal omics Python framework

anndata2ri

Convert between AnnData and SingleCellExperiment

cirrocumulus

Bring your single-cell data to life

adpbulk

pseudobulking on an AnnData object

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

checkatlas

One liner tool to check the quality of your single-cell atlases.

cytetype

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

mllmcelltype

A Python module for cell type annotation using various LLMs.

fgread

Module for reading datasets shared on FASTGenomics

treedata

anndata with trees

flashdeconv

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

mousipy

Python package for translating between single-cell count data with mouse and human genes using orthologs from biomart and HCOP.

mudatasets

Multimodal datasets, in MuData format

pybanksy

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

llm-sc-curator

Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs.

scagg

Pseudobulk and metacell aggregation for single-cell RNA-seq (AnnData/scanpy + Seurat/R)

ncem

ncem. Learning cell communication from spatial graphs of cells.

flashs

Flash-S: Frequency-domain Linearized Adaptive Spatial Hypothesis testing via Sketching

pycea-lineage

Scverse lineage tracing toolkit

orthomap

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

sobolev-alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles