ArticleNature methods2025
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed.
- Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- MuSpAn: a toolbox for multiscale spatial analysis.Nature communications · 2026Article
- SpatialFlux: an R package for distance gradient analysis in spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Single-cell transcriptome reveals keratinocyte subclusters contributing to altered differentiation and inflammatory responses in atopic dermatitis.Nature communications · 2026Article
- D3aist: data-driven detection of atypical interactions in spatial transcriptomics.BMC genomics · 2026Article
- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- SPEAK: Spatial Prompting with Expert Aligned Knowledge for Tissue Domain Identification in Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- A Counterfactual Framework for Directional Cell-Cell Interaction Analysis in Spatial Transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Review
- geneSCOPE: gene spatial co-occurrence of pairwise expression.Briefings in bioinformatics · 2026Article
- SPOmiAlign: a modality-agnostic computational framework for multimodal spatial omics alignment enabled by a feature matching foundation model.Briefings in bioinformatics · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Spatially Anchored Regulatory State Inference in Melanoma.bioRxiv : the preprint server for biology · 2026Article
- CosMxScope: Scalable Reconstruction and Digital Pathology Integration of Imaging-Based Spatial Transcriptomics Data.bioRxiv : the preprint server for biology · 2026Article
- Exploring the human brain: spatial transcriptomics challenges and approaches in post-mortem analysis.Brain : a journal of neurology · 2026Review
- HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps.Nature communications · 2026Article
- MANTIS: Analytics toolkit for spatial metabolomics with matching spatial transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- Mapping multipathology via spatial omic integration.Current opinion in biotechnology · 2026Review
- Article
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Authors and funding
16 authors.
Funding
Abstract
Emerging spatial multiomics technologies provide an increasingly large amount of information content at multiple scales. However, it remains challenging to efficiently represent and harmonize diverse spatial datasets. Here we present Giotto Suite, a suite of modular packages that provides scalable and extensible end-to-end solutions for multiscale and multiomic data analysis, integration and visualization. At its core, Giotto Suite is centered around an innovative data framework, allowing the representation and integration of spatial omics data in a technology-agnostic manner. Giotto Suite integrates molecular, morphology, spatial and annotated feature information to create a responsive and flexible workflow, as demonstrated by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science in R, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive and multiscale ecosystem for spatial multiomic data analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.