Spatial Transcriptomics Python Packages | PyRank

squidpy

Spatial Single Cell Analysis in Python

55K 569 113

decoupler

Python package to perform enrichment analysis from omics data.

50K 268 36

sopa

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

5K 277 50

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

3K 37 9

spagcn

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

3K 261 67

revise-svc

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

2K 25 0

enrichmap

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

2K 15 4

spatialquery

Efficient tool to query spatial pattern of spatial-modalities data

2K 5 1

novae

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

2K 130 13

sccellfie

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

2K 61 4

effidict

Develop custom oligo design pipelines.

2K 28 7

oligo-designer-toolsuite

Develop custom oligo design pipelines.

1K 28 7

bellavista

Python package for interactive visualization of imaging-based spatial transcriptomics

1K 7 2

spatialprofilingtoolbox

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

1K 23 2

spatialdm

Spatial direct messaging detected by bivariate Moran

908 32 6

omero-vitessce

OMERO Vitessce multimodal data viewer plugin for OMERO.web

895 13 1

histoseg

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

853 0 0

stminer

Python package for spatial transcriptomics data analysis

823 18 7

pathml

Tools for computational pathology

730 452 89

gps-mapping

Genetics-informed pathogenic spatial mapping

725 204 16

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

697 6 2

cytocraft

The Cytocraft package provides 3D reconstruction of spatial configuration of transcription centers

670 0 0

gsmap

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

640 206 16

flashdeconv

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

582 18 0