Search Packages

spotsweeper

Spatially-aware quality control for spatial transcriptomics

decoupler

Python package to perform enrichment analysis from omics data.

squidpy

Spatial Single Cell Analysis in Python

sopa

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

spatialquery

Efficient tool to query spatial pattern of spatial-modalities data

novae

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

enrichmap

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

spagcn

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

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

spatialprofilingtoolbox

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

pantheon-agents

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

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

bellavista

Python package for interactive visualization of imaging-based spatial transcriptomics

torchgw

Fast Sampled Gromov-Wasserstein optimal transport solver — pure PyTorch, scalable, differentiable

pathml

Tools for computational pathology

pciseq

A probabilistic cell typing algorithm for spatial transcriptomics.

sccellfie

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

effidict

Develop custom oligo design pipelines.

revise-svc

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

omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

gsmap

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

spatialdm

Spatial direct messaging detected by bivariate Moran

gps-mapping

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

histoseg

Python toolkit for H&E image analysis and spatial contour analysis.