Giotto Current Protocols

Giotto is an R package for the analysis and visualization of spatial transcriptomics. The underlying framework is generalizeable to virtually all currently available spatial datasets

This respository contains supplemental R markdown files to be paired with our manuscript “Analyzing Spatial Transcriptomics Data Using Giotto” (Current Protocols).

Scripts and analyses

In-depth markdown containing the code used to generate the analyses and figures in the manuscript and code used to generate the single cell annotations. Explanations are given for each step of the process.

Markdown containing only the scripts that are present in the manuscript code windows. Supplementary data and analyses are read in (full processing can be found in cp_walkthrough.Rmd). Each chunk of code is numbered based on order of appearance in the manuscript. This R markdown is meant to facilitate the running of the code as shown in the manuscript. Colors may differ from final figures because they were not expressly set due to the abridged nature of the manuscript code.


  • Del Rossi, N., Chen, J. G., Yuan, G. C., & Dries, R. (2022). Analyzing Spatial Transcriptomics Data Using Giotto. Current protocols, 2(4), e405.