Spatial Transcriptomics Python Packages

squidpy

Spatial Single Cell Analysis in Python

decoupler

Python package to perform enrichment analysis from omics data.

spagcn

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

stpipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

sopa

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

biomedical-ai-skills

AI agent skills for cancer biology and multi-omics research

laris

LARIS maps ligand-receptor signalling in spatial transcriptomics within and across tissue states

cytome

Single-file format for single-cell multi-omics and spatial transcriptomics — matrices, metadata, embeddings, fragments and provenance in one SQLite-backed .cytome file, with SQL metadata queries and genomic range indexes.

autozyme

Autonomous multi-agent framework to optimize scientific software

novae

Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

batchlens-bio

Metadata-only experimental-design and batch-confounding audits for single-cell and spatial studies

spatialexperiment

Container for Spatial Experiments

piaso-mcp

Agent-neutral knowledge hub that makes the PIASO single-cell omics ecosystem (PIASO, COSG/COSGR, LARIS, Emergene, PIASOmarkerDB) first-class for any coding agent. One canonical source generates Claude skills, Cursor rules, AGENTS.md, llms.txt, and an MCP server.

oligo-designer-toolsuite

Develop custom oligo design pipelines.

pantheon-agents

A general, evolvable, and distributed agent framework & harness for data science.

pybanksy

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

cosg

Accurate and fast cell marker gene identification with COSG

flashdeconv

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

revise-svc

REVISE is a Python toolkit for reconstruct and analyse spatial transcriptomics (ST) data at single-cell resolution across diverse ST platforms.

spatialquery

Efficient tool to query spatial pattern of spatial-modalities data

effidict

Develop custom oligo design pipelines.

enrichmap

EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics.