A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
☆165Mar 16, 2026Updated 3 weeks ago
Alternatives and similar repositories for cellcharter
Users that are interested in cellcharter are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- End-to-end analysis of spatial multi-omics data☆108Jan 26, 2026Updated 2 months ago
- BANKSY: spatial clustering☆139Oct 15, 2025Updated 5 months ago
- ☆53Oct 9, 2025Updated 6 months ago
- a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution☆53Aug 11, 2025Updated 8 months ago
- ☆134Apr 24, 2024Updated last year
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- Spatial Single-Cell Analysis Toolkit☆110Mar 11, 2026Updated 3 weeks ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆268Apr 3, 2026Updated last week
- ☆13Jun 6, 2024Updated last year
- Gene group activity utility functions for Scanpy☆101Dec 21, 2024Updated last year
- Spatial Single Cell Analysis in Python☆560Updated this week
- A tool for semi-automatic cell type harmonization and integration☆120Mar 9, 2026Updated last month
- Probabilistic cell segmentation for in situ spatial transcriptomics☆164Mar 13, 2026Updated 3 weeks ago
- LIANA+: an all-in-one framework for cell-cell communication☆281Jan 24, 2026Updated 2 months ago
- Join subcellular Visium HD bins into cells☆138Nov 4, 2025Updated 5 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- An open and interoperable data framework for spatial omics data☆359Mar 30, 2026Updated last week
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆448Jan 22, 2026Updated 2 months ago
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆34Jul 24, 2025Updated 8 months ago
- Multi-omic single-cell optimal transport tools☆200Updated this week
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆48Aug 18, 2025Updated 7 months ago
- Automatically annotate cell types, consistently across samples.☆20Updated this week
- CellRank: dynamics from multi-view single-cell data☆437Updated this week
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆184Aug 12, 2025Updated 7 months ago
- Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms☆48Oct 22, 2025Updated 5 months ago
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- A novel machine learning pipeline to analyse spatial transcriptomics data☆244Mar 12, 2026Updated 3 weeks ago
- A Bayesian model for compositional single-cell data analysis☆194Jan 13, 2026Updated 2 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆238Aug 7, 2024Updated last year
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆139Feb 20, 2025Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆424Sep 4, 2025Updated 7 months ago
- Analyzing cellular niches in spatial transcriptomics data☆34Nov 18, 2024Updated last year
- A collection of project templates and useful functions for single-cell data analysis with Scanpy.☆21Jun 12, 2023Updated 2 years ago
- Python API and Jupyter widget for Vitessce☆65Updated this week
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆349Mar 31, 2026Updated last week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆91Dec 8, 2022Updated 3 years ago
- CAST package☆43Oct 26, 2024Updated last year
- ☆65Updated this week
- Spatial alignment of single cell transcriptomic data.☆361Jul 1, 2025Updated 9 months ago
- Static plotting for spatialdata☆76Apr 3, 2026Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆88Nov 16, 2025Updated 4 months ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆95Dec 11, 2023Updated 2 years ago