Giotto Documentation

Brief introduction

Giotto contains two independent yet fully integrated parts. The first part (Giotto Analyzer) is a R package that provides utilities and step-by-step instructions about the different steps in analyzing spatial single-cell data. The second part (Giotto Viewer), which is a web-based server, provides a fast and interactive viewer of spatial single-cell data and additional annotations (such as stainings, morphology and subcellular transcript localization information). These two parts can be used either independently or iteratively.

Giotto Analyzer tutorials

Tutorial 1 Dimensionality reduction, clustering, marker gene identification
Tutorial 2 Spatial gene detection
Tutorial 3 Spatial pattern mining
Tutorial 4 Cell-cell proximity analysis
Tutorial 5 Virtual slicing, 3D visualization
Tutorial 6 Cell type enrichment
Get details from Github repository

Giotto Viewer tutorials

Tutorial 1 Launch a docker terminal (docker users)
Tutorial 2 Set up a dataset for viewing (3 modes: no images, with images, or with images and segmentations)
More info including a live demo
Browse the viewer usage manual