Scanpy Python Packages

anndata

Annotated data.

scanpy

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

anndata2ri

Convert between AnnData and SingleCellExperiment

muon

muon is a multimodal omics Python framework

autozyme

Autonomous multi-agent framework to optimize scientific software

adpbulk

pseudobulking on an AnnData object

checkatlas

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

cirrocumulus

Bring your single-cell data to life

cytetype

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

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

mllmcelltype

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

treedata

anndata with trees

fgread

Python readers for different data formats for FASTGenomics.

pybanksy

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

cell-gps

Cell-GPS spatial topology analysis for spatial omics data.

mousipy

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

scagg

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

flashdeconv

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

mudatasets

Multimodal datasets, in MuData format

llm-sc-curator

Dynamic feature distillation framework for robust zero-shot LLM annotation.

ncem

ncem. Learning cell communication from spatial graphs of cells.

flashs

Spatially variable gene detection via frequency-domain kernel testing

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.

pycea-lineage

Scverse lineage tracing toolkit