ArticleGenome biology2021
Giotto: a toolbox for integrative analysis and visualization of spatial expression data.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 628 papers, 1 of them a synthesis that pooled it.
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Who cites it
628 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.Genome biology · 2025Pooled it
- Multimodal assessment of exceptional responders refines subtyping-directed precision treatment in HR+/HER2- breast cancer.The Journal of clinical investigation · 2026Trial
- SpatialZoomer: multi-scale feature analysis of spatial transcriptomics.Nature biomedical engineering · 2026Article
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- Article
- Ten quick tips for spatial transcriptomics analysis.PLoS computational biology · 2026Review
- Iterative multiplex imaging cytometry for cross-species analyses of in situ tissue leukocytes.Journal of immunological methods · 2026Article
- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- Iron-catalyzed oxidative stress reveals an exposome-related ferroptosis-resistant karyomegalic niche in BRCA1-linked renal carcinogenesis.Redox biology · 2026Article
- A multiperspective evaluation framework of spatial transcriptomics clustering methods.NAR genomics and bioinformatics · 2026Article
- Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover.Nature genetics · 2026Article
- Halo: a pretrained model for whole-cell segmentation from nuclei images in spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- Spatial cell-cell communication inference based on cell-spot-ligand-receptor heterogeneous graphs.PLoS computational biology · 2026Article
- SemanticST: A Scalable Multi-Contextual Graph Learning Framework for Uncovering Spatial Niches and Robust Multi-Sample Integration in Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies.Cell reports methods · 2026Article
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- Tissue and cellular spatiotemporal dynamics in colon aging.Nature biotechnology · 2026Article
- DESpace2: detection of differential spatial patterns in spatial omics data.Bioinformatics (Oxford, England) · 2026Article
568 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
Abstract
Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.
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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.