Spatial Transcriptomics Python Packages

squidpy

Spatial Single Cell Analysis in Python

decoupler

Python package to perform enrichment analysis from omics data.

autozyme

Autonomous multi-agent framework to optimize scientific software

sopa

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

spagcn

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

novae

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

revise-svc

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

enrichmap

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

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

sdeper

Spatial Deconvolution method with Platform Effect Removal

omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

effidict

Develop custom oligo design pipelines.

spatialquery

Spatial query tools for analyzing spatial transcriptomics data

oligo-designer-toolsuite

Develop custom oligo design pipelines.

pathml

Tools for computational pathology

gsmap

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

pantheon-agents

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

spatialprofilingtoolbox

Toolbox for spatial analysis of single cell data.

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

pybanksy

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

sccellfie

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

cosg

Accurate and fast cell marker gene identification with COSG

bellavista

Python package for interactive visualization of imaging-based spatial transcriptomics

stminer

Python package for spatial transcriptomics data analysis