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Spatial Transcriptomics Python Packages

Python packages with the GitHub topic spatial-transcriptomics. Sorted by relevance, with stars and monthly downloads.
danielchen05
spotsweeper

Spatially-aware quality control for spatial transcriptomics

539K 9 0
scverse
decoupler

Python package to perform enrichment analysis from omics data.

50K 267 36
scverse
squidpy

Spatial Single Cell Analysis in Python

43K 567 114
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 275 49
ShaokunAn
spatialquery

Efficient tool to query spatial pattern of spatial-modalities data

3K 4 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 129 12
jianhuupenn
spagcn

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

2K 260 67
secrierlab
enrichmap

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

2K 13 4
cafferychen777
chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

2K 34 8
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
nadeemlab
spatialprofilingtoolbox

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

1K 23 2
aristoteleo
pantheon-agents

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

1K 412 57
chansigit
torchgw

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

1K 1 0
pkosurilab
bellavista

Python package for interactive visualization of imaging-based spatial transcriptomics

1K 7 2
earmingol
sccellfie

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

1K 57 3
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

1K 6 2
Dana-Farber-AIOS
pathml

Tools for computational pathology

1K 451 89
HelmholtzAI-Consultants-Munich
effidict

Develop custom oligo design pipelines.

1K 28 7
MicheleBortol
omero-vitessce

OMERO.web plugin for the Vitessce multimodal data viewer.

1K 13 1
acycliq
pciseq

A probabilistic cell typing algorithm for spatial transcriptomics.

1K 25 8
xjtu-omics
stminer

Python package for spatial transcriptomics data analysis

950 17 7
JianYang-Lab
gsmap

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

902 204 16
StatBiomed
spatialdm

Spatial direct messaging detected by bivariate Moran

889 31 6
hutaobo
histoseg

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

871 0 0
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