☆74May 28, 2025Updated last year
Alternatives and similar repositories for SpatialExperiment
Users that are interested in SpatialExperiment are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.☆183Jan 8, 2026Updated 7 months ago
- Spatial omics analysis toolbox☆388Updated this week
- Spatial Transcriptomics Capture Location Deconvolution☆212Oct 20, 2025Updated 10 months ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆89Nov 16, 2025Updated 9 months ago
- Multi-omics studies are available here☆53Jul 3, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- TRAjectory-based Differential Expression analysis for SEQuencing data☆310Jun 17, 2025Updated last year
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆114Updated this week
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆19Sep 19, 2025Updated 11 months ago
- ☆12May 29, 2024Updated 2 years ago
- Extension of SpatialExperiment with sf☆57May 6, 2026Updated 3 months ago
- Multiview Intercellular SpaTial modeling framework☆74Jan 15, 2026Updated 7 months ago
- "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book☆114Jul 11, 2026Updated last month
- Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.…☆49Sep 29, 2025Updated 11 months ago
- A simple and performant native R reader & writer for Zarr Arrays☆54Aug 21, 2026Updated last week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Interpretation of cell states using reference single-cell maps☆323Dec 19, 2025Updated 8 months ago
- R vignettes for processing BUS format single-cell RNA-seq files☆21Feb 8, 2020Updated 6 years ago
- A performant scientific image visualization system.☆36Aug 5, 2026Updated 3 weeks ago
- ☆12Updated this week
- R API and htmlwidget for Vitessce☆46Aug 13, 2025Updated last year
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆481Jan 22, 2026Updated 7 months ago
- A Toolbox for Spatial Transcriptomics Analysis☆173May 6, 2025Updated last year
- ☆13Apr 27, 2022Updated 4 years ago
- Gene group activity utility functions for Scanpy☆117Dec 21, 2024Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- ☆38Aug 15, 2026Updated 2 weeks ago
- LIANA: a LIgand-receptor ANalysis frAmework☆247Aug 7, 2024Updated 2 years ago
- Interoperability between SpatialData and the Xenium Explorer☆26Jul 31, 2024Updated 2 years ago
- From geospatial to spatial -omics☆103Jul 24, 2026Updated last month
- ☆35Jul 17, 2026Updated last month
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Jun 13, 2025Updated last year
- ☆30Oct 4, 2024Updated last year
- ☆32Jan 7, 2026Updated 7 months ago
- Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).☆23Sep 29, 2025Updated 11 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.
- End-to-end pipeline for segmenting cell nuclei on histology slides☆16Jul 19, 2022Updated 4 years ago
- code for composite in situ imaging (cisi) analysis☆12Oct 26, 2020Updated 5 years ago
- The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…☆43Feb 5, 2026Updated 6 months ago
- Learning cell communication from spatial graphs of cells☆121Jan 15, 2024Updated 2 years ago
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆16Feb 27, 2026Updated 6 months ago
- Code for the spatialLIBD R/Bioconductor package and shiny app☆113Jul 24, 2026Updated last month
- Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R☆19Aug 20, 2026Updated last week