Merge pull request #852 from josschavezf/suite

update readme
drieslab · Jan 3, 2024 · 81acf1e · 81acf1e
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diff --git a/README.Rmd b/README.Rmd
@@ -22,39 +22,28 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/drieslab/Giotto/actions/workflows/main_check.yaml/badge.svg?branch=suite)](https://github.com/drieslab/Giotto/actions/workflows/main_check.yaml)
 <!-- badges: end -->
 
-Giotto Suite is a collection of open source software tools, including data structures and methods, for the comprehensive analysis and visualization of spatial multi-omics data at multiple scales and resolutions. It extends and improves our previous R package [Giotto](https://github.com/drieslab/Giotto/tree/master). The underlying framework of Giotto Suite is generalizable to virtually all current and emerging spatial technologies which may differ in resolution (e.g. subcellular, single cell, or multiple cells), spatial dimension (i.e. 2D vs. 3D), molecular modality (e.g. protein, RNA, DNA, …), and throughput (i.e. number of cells and analytes). Giotto Suite is designed to ensure spatial analysis solutions remain compatible with current and future spatial -omics technologies and platforms. It will also aid in the further integration of spatial -omics with external analysis pipelines and tools.
+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).
 
-**Repository Changes!**
-With the release of [v3.4.0](https://github.com/drieslab/Giotto/releases/tag/v3.4.0), Giotto Suite has become modularized. We have divided Giotto Suite into several smaller packages:
-- [GiottoUtils](https://github.com/drieslab/GiottoUtils)
-- [GiottoClass](https://github.com/drieslab/GiottoClass)
-- [GiottoVisuals](https://github.com/drieslab/GiottoVisuals)
-We've done this to ease maintainance, to have clearer categorizations for different functionalities, and to make the Suite easier to explore. Further, this separates dependencies and helps efforts to conform with size requirements for mirrors (e.g. BioConductor).
 
-**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.
+## Installation
 
-**Github Repository changes!**  
-The Giotto github repository has moved to https://github.com/drieslab/Giotto and the associated spatial datasets have been moved to https://github.com/drieslab/spatial-datasets. 
+To install Giotto suite use
+`devtools::install_github("drieslab/Giotto")`. 
 
-**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/
+Visit the Giotto [Discussions](https://github.com/drieslab/Giotto/discussions) page for more information.
 
-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). 
+## Website description  
 
-The package is in heavy development. Please check back often!  
-For a version history/changelog, please see the [NEWS file](https://github.com/drieslab/Giotto/blob/suite/NEWS.md).
-
-<!-- <img src="inst/images/general_figs/overview_datasets.png" /> -->
+- **Get started:** Here you can find more advanced information about the Giotto object, Giotto ecosystem, Giotto configuration, and installation FAQs.
+- **Documentation:** Here you will find all Giotto functions grouped by their purpose (Helpers, Getters & Setters, Visualization, ...)
+- **Examples:** Here you can find end-to-end  examples for different technologies and datasets.
+- **Tutorials:** Here you can find various tutorials on working with Giotto (analysis, visualizations, working on the cloud, ...)
+- **News:** Here you can find the changelog for every Giotto release and video recordings from previous presentations. 
 
 ## 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}
-
-
-
+- [Jiaji George Chen, Joselyn Cristina Chávez-Fuentes, et al. Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem. bioRxiv (2023).](https://www.biorxiv.org/content/10.1101/2023.11.26.568752v1)
+- [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)
+- [Dries, R., Chen, J. et al. Advances in spatial transcriptomic data analysis. Genome Research (2021).](https://genome.cshlp.org/content/31/10/1706.long)
+- [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)
 
diff --git a/README.md b/README.md
@@ -15,66 +15,29 @@ Latest](https://img.shields.io/github/commits-since/drieslab/Giotto/latest/suite
 [![R-CMD-check](https://github.com/drieslab/Giotto/actions/workflows/main_check.yaml/badge.svg?branch=suite)](https://github.com/drieslab/Giotto/actions/workflows/main_check.yaml)
 <!-- badges: end -->
 
-**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.
+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).
 
-**Github Repository changes!**  
-The Giotto github repository has moved to
-<https://github.com/drieslab/Giotto> and the associated spatial datasets
-have been moved to <https://github.com/drieslab/spatial-datasets>.
 
-**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/>
+## Installation
 
-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
+`devtools::install_github("drieslab/Giotto")`. 
 
-The package is in heavy development. Please check back often!  
-For a version history/changelog, please see the [NEWS
-file](https://github.com/drieslab/Giotto/blob/suite/NEWS.md).
+Visit the Giotto [Discussions](https://github.com/drieslab/Giotto/discussions) page for more information.
+
+## Website description  
+
+- **Get started:** Here you can find more advanced information about the Giotto object, Giotto ecosystem, Giotto configuration, and installation FAQs.
+- **Documentation:** Here you will find all Giotto functions grouped by their purpose (Helpers, Getters & Setters, Visualization, ...)
+- **Examples:** Here you can find end-to-end  examples for different technologies and datasets.
+- **Tutorials:** Here you can find various tutorials on working with Giotto (analysis, visualizations, working on the cloud, ...)
+- **News:** Here you can find the changelog for every Giotto release and video recordings from previous presentations. 
 
 <!-- <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)
-- [Dries, R., Chen, J. et al. Advances in spatial transcriptomic data
-  analysis. Genome Research
-  (2021).](https://genome.cshlp.org/content/31/10/1706.long)
-- [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)
+- [Jiaji George Chen, Joselyn Cristina Chávez-Fuentes, et al. Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem. bioRxiv (2023).](https://www.biorxiv.org/content/10.1101/2023.11.26.568752v1)
+- [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)
+- [Dries, R., Chen, J. et al. Advances in spatial transcriptomic data analysis. Genome Research (2021).](https://genome.cshlp.org/content/31/10/1706.long)
+- [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)