Scanpy Python Packages

anndata

Annotated data.

scanpy

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

marsilea

Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

muon

muon is a multimodal omics Python framework

ambidose

AmbiDose is a conservative, cell-aware Python toolkit for ambient RNA correction in droplet scRNA-seq. It estimates sample-specific ambient profiles and per-cell doses, protects native cell-type signals, preserves sparsity, and never inflates counts.

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

adpbulk

pseudobulking on an AnnData object

cirrocumulus

Bring your single-cell data to life

spatioloji-s

Python toolkit for image-based spatial transcriptomics (CosMx, MERFISH, Xenium). Unified data object for expression, polygons, and FOV images, plus QC, clustering, point- and polygon-based spatial statistics, and polygon-native cell-cell communication using real membrane contact geometry.

biomedical-ai-skills

AI agent skills for cancer biology and multi-omics research

anndata2ri

Convert between AnnData and SingleCellExperiment

checkatlas

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

cytetype

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

autozyme

Autonomous multi-agent framework to optimize scientific software

pybanksy

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

flashdeconv

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

clonetrast

CloneTrast reveals pan-cancer clonal niches of T-cells from single-cell RNA sequencing using contrastive learning

fgread

Python readers for different data formats for FASTGenomics.

scfair

 scFair: a seamless Python alternative for scanpy.pp.highly_variable_genes that fixes two silent failures in single-cell HVG selection — no more guessing gene count (auto-sized n_top_genes) and no more losing rare cell-type markers to majority-biased ranking (smart top-k extension).

mllmcelltype

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

llm-sc-curator

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

pycea-lineage

scverse lineage tracing analysis toolkit

flashs

Spatially variable gene detection via frequency-domain kernel testing

mousipy

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