Giotto Suite is a major upgrade to the Giotto package that provides tools to process, analyze and visualize spatial multi-omics data at all scales and multiple resolutions. The underlying framework is generalizable to virtually all current and emerging spatial technologies. Our Giotto Suite prototype pipeline is generally applicable on various different datasets, such as those created by state-of-the-art spatial technologies, including in situ hybridization (seqFISH+, merFISH, osmFISH, CosMx), sequencing (Slide-seq, Visium, STARmap, Seq-Scope, Stereo-Seq) and imaging-based multiplexing/proteomics (CyCIF, MIBI, CODEX). These technologies differ in terms of resolution (subcellular, single cell or multiple cells), spatial dimension (2D vs 3D), molecular modality (protein, RNA, DNA, …), and throughput (number of cells and analytes).
To install Giotto suite use pak::pkg_install("drieslab/Giotto")
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Visit the Giotto Discussions page for more information.
With Giotto version 4.0, we updated the website at http://giottosuite.com, you can still find the previous website at https://giottosuite.readthedocs.io/en/latest/
This software project was supported in part by the Essential Open Source Software for Science (EOSS) program at Chan Zuckerberg Initiative.