A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
☆186Aug 10, 2026Updated this week
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☆123May 15, 2026Updated 2 months ago
- a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution☆55Aug 11, 2025Updated last year
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆290Jul 15, 2026Updated 3 weeks ago
- BANKSY: spatial clustering☆159May 30, 2026Updated 2 months ago
- ☆143Jun 25, 2026Updated last month
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Probabilistic cell segmentation for in situ spatial transcriptomics☆183Updated this week
- LIANA+: an all-in-one framework for cell-cell communication☆309Updated this week
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆23Jun 10, 2025Updated last year
- Differential spatial enrichment across conditions☆28Jul 14, 2026Updated last month
- An open and interoperable data framework for spatial omics data☆383Updated this week
- Spatial Single-Cell Analysis Toolkit☆113Mar 11, 2026Updated 5 months ago
- ☆55Updated this week
- Static plotting for spatialdata☆82Updated this week
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆87Jul 4, 2026Updated last month
- 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-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆477Jan 22, 2026Updated 6 months ago
- Spatial Single Cell Analysis in Python☆589Updated this week
- A Bayesian model for compositional single-cell data analysis☆199Jan 13, 2026Updated 7 months ago
- Gene group activity utility functions for Scanpy☆115Dec 21, 2024Updated last year
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆152Feb 20, 2025Updated last year
- Spatial alignment of single cell transcriptomic data.☆370Jul 1, 2025Updated last year
- A tool for semi-automatic cell type harmonization and integration☆121Mar 9, 2026Updated 5 months ago
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆50Aug 18, 2025Updated 11 months ago
- Python package to perform enrichment analysis from omics data.☆288Updated this week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Profile purification of single-cell spatial transcriptomics data☆51Jun 29, 2026Updated last month
- Spatial omics analysis toolbox☆387Updated this week
- Multi-omic single-cell optimal transport tools☆215Updated this week
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆195Aug 12, 2025Updated last year
- Join subcellular Visium HD bins into cells☆143May 8, 2026Updated 3 months ago
- Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms☆50Oct 22, 2025Updated 9 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆247Aug 7, 2024Updated 2 years ago
- Package for the analysis of Transcripts outside segmented cells in ST data☆31Updated this week
- rapids-singlecell: GPU-accelerated framework for scRNA analysis☆390Updated this week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆463Apr 11, 2026Updated 4 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆442May 11, 2026Updated 3 months ago
- CellRank: dynamics from multi-view single-cell data☆454Aug 3, 2026Updated last week
- NicheNet: predict active ligand-target links between interacting cells☆671Jun 1, 2026Updated 2 months ago
- Morphology-Enhanced Spatial Transcriptome Analysis Integrator☆27Mar 16, 2025Updated last year
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆148Jul 8, 2026Updated last month
- From geospatial to spatial -omics☆103Jul 24, 2026Updated 3 weeks ago