Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
☆449Jan 22, 2026Updated 3 months ago
Alternatives and similar repositories for spacexr
Users that are interested in spacexr are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆429Updated this week
- Spatial Transcriptomics Capture Location Deconvolution☆205Oct 20, 2025Updated 6 months ago
- BANKSY: spatial clustering☆141Oct 15, 2025Updated 6 months ago
- Spatial omics analysis toolbox☆372Updated this week
- A Toolbox for Spatial Transcriptomics Analysis☆166May 6, 2025Updated 11 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 mapping of cell types by integration of transcriptomics data☆100Updated this week
- ☆129Mar 27, 2022Updated 4 years ago
- Spatial alignment of single cell transcriptomic data.☆361Jul 1, 2025Updated 9 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆428Apr 23, 2026Updated last week
- Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data☆154Aug 3, 2025Updated 8 months ago
- Spatiotemporal modeling of spatial transcriptomics☆336Feb 25, 2026Updated 2 months ago
- Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.☆176Jan 8, 2026Updated 3 months ago
- High dimensional weighted gene co-expression network analysis☆472Mar 13, 2026Updated last month
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆185Aug 12, 2025Updated 8 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- CellRank: dynamics from multi-view single-cell data☆443Updated this week
- ☆132Feb 11, 2024Updated 2 years ago
- LIANA: a LIgand-receptor ANalysis frAmework☆239Aug 7, 2024Updated last year
- A novel machine learning pipeline to analyse spatial transcriptomics data☆245Apr 17, 2026Updated 2 weeks ago
- R package to infer biological activities from omics data using a collection of methods.☆292Dec 16, 2025Updated 4 months ago
- Join subcellular Visium HD bins into cells☆140Nov 4, 2025Updated 5 months ago
- ☆137Apr 24, 2024Updated 2 years ago
- ☆280Oct 13, 2025Updated 6 months ago
- A tool for semi-automatic cell type classification☆473Mar 21, 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.
- NicheNet: predict active ligand-target links between interacting cells☆639Nov 12, 2025Updated 5 months ago
- ☆99Apr 16, 2026Updated 2 weeks ago
- Inferring CNV from Single-Cell RNA-Seq☆663Nov 14, 2025Updated 5 months ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆141Feb 20, 2025Updated last year
- ☆147Mar 20, 2026Updated last month
- Multi-sample multi-group scRNA-seq analysis tools☆226Apr 11, 2026Updated 2 weeks ago
- A toolkit of spatial transcriptomic analysis.☆277Apr 7, 2026Updated 3 weeks ago
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Learning cell communication from spatial graphs of cells☆116Jan 15, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆114Jun 9, 2025Updated 10 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆92Dec 8, 2022Updated 3 years ago
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆275Apr 23, 2026Updated last week
- Bayesian Segmentation of Spatial Transcriptomics Data☆204Apr 23, 2026Updated last week
- Code for the spatialLIBD R/Bioconductor package and shiny app☆112Mar 27, 2026Updated last month
- Spatial Single Cell Analysis in Python☆566Updated this week
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆121Jan 22, 2024Updated 2 years ago