☆72May 28, 2025Updated 9 months ago
Alternatives and similar repositories for SpatialExperiment
Users that are interested in SpatialExperiment are comparing it to the libraries listed below
Sorting:
- Spatial omics analysis toolbox☆362Feb 12, 2026Updated last month
- Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.☆169Jan 8, 2026Updated 2 months ago
- Spatial Transcriptomics Capture Location Deconvolution☆203Oct 20, 2025Updated 4 months ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆88Nov 16, 2025Updated 4 months ago
- Multi-omics studies are available here☆53Jul 3, 2022Updated 3 years ago
- TRAjectory-based Differential Expression analysis for SEQuencing data☆291Jun 17, 2025Updated 9 months ago
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆17Sep 19, 2025Updated 6 months ago
- Gene group activity utility functions for Scanpy☆100Dec 21, 2024Updated last year
- ☆12May 29, 2024Updated last year
- Extension of SpatialExperiment with sf☆57Mar 7, 2026Updated last week
- A performant scientific image visualization system.☆36Updated this week
- "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book☆107Mar 11, 2026Updated last week
- Multiview Intercellular SpaTial modeling framework☆72Jan 15, 2026Updated 2 months ago
- R vignettes for processing BUS format single-cell RNA-seq files☆21Feb 8, 2020Updated 6 years ago
- A simple native R reader for Zarr Arrays☆48Updated this week
- Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.…☆48Sep 29, 2025Updated 5 months ago
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆97Mar 12, 2026Updated last week
- ☆21Updated this week
- Interpretation of cell states using reference single-cell maps☆313Dec 19, 2025Updated 3 months ago
- ☆11Feb 24, 2026Updated 3 weeks ago
- Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …☆444Jan 22, 2026Updated last month
- R API and htmlwidget for Vitessce☆44Aug 13, 2025Updated 7 months ago
- A Toolbox for Spatial Transcriptomics Analysis☆166May 6, 2025Updated 10 months ago
- Single-cell spatial omics analysis that makes you happy!☆52Updated this week
- ☆13Apr 27, 2022Updated 3 years ago
- LIANA: a LIgand-receptor ANalysis frAmework☆234Aug 7, 2024Updated last year
- Interoperability between SpatialData and the Xenium Explorer☆25Jul 31, 2024Updated last year
- From geospatial to spatial -omics☆101Mar 11, 2026Updated last week
- Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R☆17Dec 18, 2024Updated last year
- ☆32Jan 7, 2026Updated 2 months ago
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Jun 13, 2025Updated 9 months ago
- ☆30Oct 4, 2024Updated last year
- Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).☆24Sep 29, 2025Updated 5 months ago
- End-to-end pipeline for segmenting cell nuclei on histology slides☆16Jul 19, 2022Updated 3 years ago
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆15Feb 27, 2026Updated 2 weeks ago
- ☆33Updated this week
- code for composite in situ imaging (cisi) analysis☆12Oct 26, 2020Updated 5 years ago
- Learning cell communication from spatial graphs of cells☆113Jan 15, 2024Updated 2 years ago
- The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…☆41Feb 5, 2026Updated last month