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README.Rmd
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---
output: github_document
---
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# Giotto
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[](https://opensource.org/licenses/MIT)
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**Default branch change!**
With the release of [v3.3.0](https://github.com/drieslab/Giotto/releases/tag/v3.3.0) the default branch of Giotto has been moved from [@master](https://github.com/drieslab/Giotto/tree/master) to [@suite](https://github.com/drieslab/Giotto/tree/suite). If you want to install the original master version use `devtools::install_github("drieslab/Giotto@master")`. Visit the Giotto [Discussions](https://github.com/drieslab/Giotto/discussions) page for more information.
**Website change!**
We have created a new [readthedocs website](https://giottosuite.readthedocs.io/en/latest/#) 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.
- www.spatialgiotto.com links to the original [master version](https://giottosuite.readthedocs.io/en/master/). The old master pkgdown documentation can still be found at https://rubd.github.io/Giotto_site/
- www.giottosuite.com links to the extended [suite version](https://giottosuite.readthedocs.io/en/latest/). The old suite pkgdown documentation can still be found at https://drieslab.github.io/Giotto_site_suite/
The Giotto package consists of two modules, Giotto Analyzer and Viewer (see [www.spatialgiotto.com](http://www.spatialgiotto.com)), which provide tools to process, analyze and visualize **single-cell spatial expression** data. The underlying framework is generalizable to virtually all currently available spatial datasets. We recently demonstrated the general applicability on 10 different datasets created by 9 different state-of-the-art spatial technologies, including *in situ* hybridization (seqFISH+, merFISH, osmFISH), sequencing (Slide-seq, Visium, STARmap) and imaging-based multiplexing/proteomics (CyCIF, MIBI, CODEX). These technologies differ in terms of resolution (single cell vs multiple cells), spatial dimension (2D vs 3D), molecular modality (protein vs RNA), and throughput (number of cells and genes).
<img src="inst/images/general_figs/overview_datasets.png" />
## References
- [Dries, R., Zhu, Q. et al. Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biology (2021).](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02286-2) \doi{10.1186/s13059-021-02286-2}
- [Dries, R., Chen, J. et al. Advances in spatial transcriptomic data analysis. Genome Research (2021).](https://genome.cshlp.org/content/31/10/1706.long) \doi{10.1101/gr.275224.121}
- [Del Rossi, N., Chen, J. et al. Analyzing Spatial Transcriptomics Data Using Giotto. Current Protocols (2022).](https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.405) \doi{10.1002/cpz1.405}