Spatial Transcriptomics Python Packages | PyPI Stats

spotsweeper

Spatially-aware quality control for spatial transcriptomics

539K 9 0

decoupler

Python package to perform enrichment analysis from omics data.

50K 267 36

squidpy

Spatial Single Cell Analysis in Python

43K 567 114

sopa

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

5K 275 49

spatialquery

Efficient tool to query spatial pattern of spatial-modalities data

3K 4 1

novae

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

2K 129 12

spagcn

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

2K 260 67

enrichmap

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

2K 13 4

chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

2K 34 8

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

spatialprofilingtoolbox

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

1K 23 2

pantheon-agents

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

1K 412 57

torchgw

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

1K 1 0

bellavista

Python package for interactive visualization of imaging-based spatial transcriptomics

1K 7 2

sccellfie

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

1K 57 3

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

1K 6 2

pathml

Tools for computational pathology

1K 451 89

effidict

Develop custom oligo design pipelines.

1K 28 7

omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

1K 13 1

pciseq

A probabilistic cell typing algorithm for spatial transcriptomics.

1K 25 8

stminer

Python package for spatial transcriptomics data analysis

950 17 7

gsmap

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

902 204 16

spatialdm

Spatial direct messaging detected by bivariate Moran

889 31 6

histoseg

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

871 0 0