Spatial Single Cell Analysis in Python
☆601Oct 7, 2026Updated this week
Alternatives and similar repositories for squidpy
Users that are interested in squidpy 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☆399Updated this week
- Single-cell analysis in Python. Scales to >100M cells.☆2,581Updated this week
- CellRank: dynamics from multi-view single-cell data☆457Updated this week
- ☆103Sep 22, 2026Updated 2 weeks ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,702Updated 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.
- Spatial alignment of single cell transcriptomic data.☆373Jul 1, 2025Updated last year
- Annotated data.☆776Updated this week
- Multimodal Data (.h5mu) implementation for Python☆134Oct 2, 2026Updated last week
- A novel machine learning pipeline to analyse spatial transcriptomics data☆259Updated this week
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆463Sep 28, 2026Updated last week
- Bayesian Segmentation of Spatial Transcriptomics Data☆216Oct 2, 2026Updated last week
- Interactive visualization of spatial omics data☆91Sep 8, 2026Updated last month
- Spatiotemporal modeling of spatial transcriptomics☆344Feb 25, 2026Updated 7 months ago
- Spatial omics analysis toolbox☆392Updated 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.
- Python package to perform enrichment analysis from omics data.☆296Updated this week
- muon is a multimodal omics Python framework☆279Updated this week
- Static plotting for spatialdata☆86Sep 28, 2026Updated last week
- Tutorials for Squidpy☆35Jul 10, 2026Updated 2 months ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆89Nov 16, 2025Updated 10 months ago
- Reference mapping for single-cell genomics☆412Jun 26, 2026Updated 3 months ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆295Sep 15, 2026Updated 3 weeks ago
- LIANA+: an all-in-one framework for cell-cell communication☆319Sep 24, 2026Updated 2 weeks ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆488Jan 22, 2026Updated 8 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- RNA Velocity generalized through dynamical modeling☆512Feb 25, 2026Updated 7 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆197Updated this week
- Learning cell communication from spatial graphs of cells☆121Jan 15, 2024Updated 2 years ago
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆400Updated this week
- A Bayesian model for compositional single-cell data analysis☆203Jan 13, 2026Updated 8 months ago
- A scanpy extension to analyse single-cell TCR and BCR data.☆266Sep 30, 2026Updated last week
- data and model repository for single-cell data☆136Dec 21, 2023Updated 2 years ago
- BANKSY: spatial clustering☆165Sep 29, 2026Updated last week
- Episcanpy: Epigenomics Single Cell Analysis in Python☆153Dec 5, 2024Updated last year
- 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.
- Python API and Jupyter widget for Vitessce☆67Sep 22, 2026Updated 2 weeks ago
- Formalizing and benchmarking open problems in single-cell genomics☆439Oct 2, 2026Updated last week
- ☆73Jan 18, 2023Updated 3 years ago
- Vitessce is a visual integration tool for exploration of spatial single-cell experiments.☆271Updated this week
- Convert between AnnData and SingleCellExperiment☆154Updated this week
- Multiple-choice microscopy pipeline☆156Sep 14, 2026Updated 3 weeks ago
- Scaling Single Cell Analysis to Millions of Cells☆307Jul 13, 2026Updated 2 months ago