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Spatial Transcriptomics Python Packages

Python packages with the GitHub topic spatial-transcriptomics. Sorted by relevance, with stars and monthly downloads.
scverse
squidpy

Spatial Single Cell Analysis in Python

55K 569 113
scverse
decoupler

Python package to perform enrichment analysis from omics data.

50K 268 36
prism-oncology
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
cafferychen777
chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

3K 37 9
jianhuupenn
spagcn

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

3K 261 67
wuys13
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
secrierlab
enrichmap

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

2K 15 4
ShaokunAn
spatialquery

Efficient tool to query spatial pattern of spatial-modalities data

2K 5 1
prism-oncology
novae

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

2K 130 13
earmingol
sccellfie

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

2K 61 4
HelmholtzAI-Consultants-Munich
effidict

Develop custom oligo design pipelines.

2K 28 7
HelmholtzAI-Consultants-Munich
oligo-designer-toolsuite

Develop custom oligo design pipelines.

1K 28 7
pkosurilab
bellavista

Python package for interactive visualization of imaging-based spatial transcriptomics

1K 7 2
nadeemlab
spatialprofilingtoolbox

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

1K 23 2
StatBiomed
spatialdm

Spatial direct messaging detected by bivariate Moran

908 32 6
MicheleBortol
omero-vitessce

OMERO Vitessce multimodal data viewer plugin for OMERO.web

895 13 1
hutaobo
histoseg

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

853 0 0
xjtu-omics
stminer

Python package for spatial transcriptomics data analysis

823 18 7
Dana-Farber-AIOS
pathml

Tools for computational pathology

730 452 89
LeonSong1995
gps-mapping

Genetics-informed pathogenic spatial mapping

725 204 16
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

697 6 2
YifeiSheng
cytocraft

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

670 0 0
JianYang-Lab
gsmap

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

640 206 16
cafferychen777
flashdeconv

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

582 18 0
    • Data from PyPI, GitHub, ClickHouse, and BigQuery