Giotto

Please visit the Giotto website to learn how to use Giotto in your spatial transcriptomics and multi-omics analysis. In this website, you will find the stable version in the master branch and the latest version in the suite branch.

Key publications:

  1. 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 ]
  2. 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. [Part 1: Giotto_CP_part1, and Part 2: Giotto_CP_part2 ) and accompanied  R Markdown]
  3. Zhu Q, Shah S, Dries R, Cai L†, Yuan GC†. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Nat Biotechnol. 2018 Oct 29;36(12):1183. [ paper ]
  4. Dong R, Yuan GC. SpatialDWLS: accurate deconvolution of spatial transcriptomic data. Genome Biol. 2021 May 10;22(1):145. [ paper ]