giotto

Parse and analyze spatial transcriptomics datasets in R with multi-platform support.

Updated Apr 19, 2026

Search Tags:#visualization #r #single-cell #giotto #spatial-analysis #spatial-genomics

Ready to run

npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill giotto

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: giotto
Source: https://github.com/CHENyiru3/AI-Skills-Collections/tree/main/skills-market/compbio/spatial-omics/analysis/giotto
Command: npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill giotto

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Giotto provides a comprehensive R toolkit for spatial genomics, enabling end-to-end analysis across multiple platforms with advanced visualization and statistics.

Core Features & Use Cases

Multi-platform support (Visium, Slide-seq, MERFISH, seqFISH, Xenium) for spatial data processing and visualization.
Create, manage, and integrate Giotto objects with single-cell references for deconvolution and comparative analyses.
Spatial networks, spatial statistics, and rich, publication-ready visualizations to reveal spatial patterns.
Reproducible workflows and best-practice guidance for end-to-end spatial transcriptomics studies.
Use cases include analyzing tissue architecture, cell-type localization, and spatially informed differential expression.

Quick Start

Install Giotto and related tooling, then start analyzing a spatial dataset with Giotto.

Frequently Asked Questions about giotto

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I perform spatial transcriptomics analysis in R across different platforms?▼

Spatial transcriptomics analysis in R is performed by creating Giotto objects to process raw counts from platforms like Visium, Slide-seq, MERFISH, seqFISH, and Xenium. This enables integrated spatial context, spatial networks, and statistics.

Does this spatial genomics toolkit support integrating single-cell references for deconvolution?▼

Yes, spatial genomics workflows support integrating single-cell references for deconvolution. You can manage and integrate Giotto objects with single-cell data to perform comparative analyses and identify cell-type localization within tissue architecture.

What is the best way to visualize spatial patterns from multi-platform spatial data?▼

The best way to visualize spatial patterns is by generating rich, publication-ready visualizations from spatial networks and statistics. This reveals spatial patterns and spatially informed differential expression across multi-platform datasets.

Can I use Giotto for end-to-end workflows from raw counts to publication-ready figures?▼

Yes, you can use Giotto for end-to-end workflows from raw counts to publication-ready figures. It provides reproducible workflows and best-practice guidance for complete spatial transcriptomics studies, satisfying spatial analysis and visualization requirements.

When do I need spatial statistics for analyzing tissue architecture?▼

Spatial statistics are needed when analyzing tissue architecture to reveal spatial patterns and perform spatially informed differential expression. These statistics integrate spatial context to identify cell-type localization within tissue datasets.

What spatial analysis tools work with seqFISH and Xenium data in R?▼

Spatial analysis tools in R like Giotto work with seqFISH and Xenium data by parsing raw counts into Giotto objects. This enables spatial data processing, spatial networks, and high-quality visualizations for these specific platforms.