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Giotto Suite

License: GPL v3 Last Commit Commits Since Latest R-CMD-check

Website change!
We have created a new readthedocs website to further improve and simplify Giotto documentation and to make it easier to use Giotto. It aggregates information from both the original Giotto package and our extended Giotto Suite, which is our extended work-in-development version.

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).

The package is in heavy development. Please check back often!

References