Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)
☆291Aug 27, 2026Updated this week
Alternatives and similar repositories for sopa
Users that are interested in sopa are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An open and interoperable data framework for spatial omics data☆387Updated this week
- Probabilistic cell segmentation for in situ spatial transcriptomics☆187Updated this week
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆155Aug 21, 2026Updated last week
- BANKSY: spatial clustering☆159May 30, 2026Updated 3 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆189Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Join subcellular Visium HD bins into cells☆143May 8, 2026Updated 3 months ago
- Code used to benchmark Xenium☆86Apr 10, 2026Updated 4 months ago
- From geospatial to spatial -omics☆103Jul 24, 2026Updated last month
- Bayesian Segmentation of Spatial Transcriptomics Data☆212Jul 31, 2026Updated 3 weeks ago
- ☆101Aug 11, 2026Updated 2 weeks ago
- Static plotting for spatialdata☆85Updated this week
- Nextflow version of Sopa - spatial omics pipeline and analysis☆19Updated this week
- Single-cell spatial omics analysis that makes you happy!☆72Updated this week
- Interactive visualization of spatial omics data☆88Aug 1, 2026Updated 3 weeks ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Interoperability between SpatialData and the Xenium Explorer☆26Jul 31, 2024Updated 2 years ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆90Jul 4, 2026Updated last month
- Automatically annotate cell types, consistently across samples.☆27Updated this week
- comseg☆24Feb 6, 2025Updated last year
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆110Updated this week
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆90May 25, 2026Updated 3 months ago
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆82Feb 10, 2026Updated 6 months ago
- Spatial Single Cell Analysis in Python☆595Updated this week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆89Nov 16, 2025Updated 9 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Spatial Single-Cell Analysis Toolkit☆115Mar 11, 2026Updated 5 months ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆31Updated this week
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆39Jul 7, 2026Updated last month
- Analyzing cellular niches in spatial transcriptomics data☆38Nov 18, 2024Updated last year
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆394Updated this week
- Differential spatial enrichment across conditions☆28Jul 14, 2026Updated last month
- A Python package for unsupervised analysis of spatial (prote)omics data.☆19Jul 23, 2026Updated last month
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆481Jan 22, 2026Updated 7 months ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆34Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems☆39Jul 11, 2025Updated last year
- Python API and Jupyter widget for Vitessce☆67Aug 10, 2026Updated 2 weeks ago
- ☆18Updated this week
- End-to-end analysis of spatial multi-omics data☆124Updated this week
- Python package to perform enrichment analysis from omics data.☆292Updated this week
- ☆236Jul 30, 2026Updated 3 weeks ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆17Jul 6, 2026Updated last month