Giotto is now Giotto Suite! It contains a suite of open-source software packages that underlies a fully modular and integrated spatial data analysis toolbox. At its core, Giotto Suite is centered around an innovative and technology-agnostic data framework embedded in the R software environment, which allows the representation and integration of virtually any type of spatial omics data at any spatial resolution. In addition, Giotto Suite provides both scalable and extensible end-to-end solutions for data analysis, integration, and visualization. Giotto Suite integrates molecular, morphology, spatial, and annotated feature information to create a responsive and flexible workflow for multi-scale, multi-omic data analyses.
Click here to access the main Giotto Suite website.
Click here for information about the original (deprecated) version of Giotto.
Giotto (Suite) is described in the following publications.
- Chen JG, Chávez-Fuentes JC, O’Brien M, Xu J, Ruiz EC, Wang W, Amin I, Sheridan JP, Shin SC, Hasyagar SV, Sarfraz I, Guckhool P, Sistig A, Jarzabek V, Yuan GC, Dries R. Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem. Nat Methods. 2025 Oct;22(10):2052-2064. [ paper ]
- Dries R*†, Zhu Q*, Dong R, Eng CL, Li H, Liu K, Fu Y, Zhao T, Sarkar A, Bao F, George RE, Pierson N, Cai L, Yuan GC†. Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biol. 2021 Mar 8;22(1):78. [ paper ]
- Del Rossi N*, Chen JG*, Yuan GC†, Dries R†. Analyzing Spatial Transcriptomics Data Using Giotto. Curr Protoc. 2022 Apr;2(4):e405. doi: 10.1002/cpz1.405. [ paper ]