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Cristianetaniguti committed Jan 8, 2024
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# VIEWpoly <img src="https://user-images.githubusercontent.com/7572527/145726577-7b01d48b-ca1d-446b-b9c8-aff8c3c9877b.png" align="right" width="230"/>

`VIEWpoly` is a shiny app and R package for visualizing and exploring results from [polyploid computational tools](https://www.polyploids.org/) using an interactive graphical user interface. The package allows users to directly upload output files from [polymapR](https://CRAN.R-project.org/package=polymapR), [MAPpoly](https://CRAN.R-project.org/package=mappoly) , [polyqtlR](https://CRAN.R-project.org/package=polyqtlR), [QTLpoly](https://CRAN.R-project.org/package=qtlpoly),
`VIEWpoly` is a shiny app and R package for visualizing and exploring results from [polyploid computational tools](https://www.polyploids.org/) using an interactive graphical user interface. The package allows users to directly upload output files from [polymapR](https://CRAN.R-project.org/package=polymapR), [MAPpoly](https://CRAN.R-project.org/package=mappoly) , [OneMap](https://github.com/Cristianetaniguti/onemap), [polyqtlR](https://CRAN.R-project.org/package=polyqtlR), [QTLpoly](https://CRAN.R-project.org/package=qtlpoly),
[diaQTL](https://github.com/jendelman/diaQTL), [GWASpoly](https://github.com/jendelman/GWASpoly), [HIDECAN](https://cran.r-project.org/web/packages/hidecan/index.html), and genomic assembly, variants, annotation and alignment files. VIEWpoly uses [shiny](https://CRAN.R-project.org/package=shiny), [golem](https://CRAN.R-project.org/package=golem), [ggplot2](https://CRAN.R-project.org/package=ggplot2), [plotly](https://CRAN.R-project.org/package=plotly), and [JBrowseR]( https://CRAN.R-project.org/package=JBrowseR) libraries to graphically display the QTL profiles, positions, alleles estimated effects, progeny individuals containing specific haplotypes and their breeding values. It is also possible to access marker dosage and parental phase from the linkage map. If genomic information is available, the corresponding QTL positions are interactively explored using JBrowseR interface, allowing the search for candidate genes. It also provides features to download specific information into comprehensive tables and images for further analysis and presentation.

### Quick Start
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You can also access `VIEWpoly` though the Docker image:

```{bash}
docker pull cristaniguti/viewpoly:0.2.1
docker run --rm -e USERID=$(id -u) -e GROUPID=$(id -g) -p 8085:80 -e DISABLE_AUTH=true cristaniguti/viewpoly:0.2.1
docker pull cristaniguti/viewpoly:0.2.2
docker run --rm -e USERID=$(id -u) -e GROUPID=$(id -g) -p 8085:80 -e DISABLE_AUTH=true cristaniguti/viewpoly:0.2.2
```

This will make the container available in port 8085 (choose other if you prefer). After, you just need to go to your favorite browser and search for <your_localhost>:8085 (example: 127.0.0.1:8085). That is it! Everything you need is there.
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* [MAPpoly](https://CRAN.R-project.org/package=mappoly)
* [polymapR](https://CRAN.R-project.org/package=polymapR)
* [OneMap](https://github.com/Cristianetaniguti/onemap)
* [polyqtlR](https://CRAN.R-project.org/package=polyqtlR)
* [QTLpoly](https://CRAN.R-project.org/package=qtlpoly)
* [diaQTL](https://github.com/jendelman/diaQTL)
@@ -99,6 +100,8 @@ Bourke PM , van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser R

Bourke PM, Voorrips RE, Hackett CA, van Geest G, Willemsen JH, Arens P, Smulders MJM, Visser RGF, Maliepaard C. 2021."Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR." Bioinformatics, 37 (21): 3822–3829, https://doi.org/10.1093/bioinformatics/btab574

Taniguti, C. H.; Taniguti, L. M.; Amadeu, R. R.; Lau, J.; de Siqueira Gesteira, G.; Oliveira, T. de P.; Ferreira, G. C.; Pereira, G. da S.; Byrne, D.; Mollinari, M.; Riera-Lizarazu, O.; Garcia, A. A. F. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12, giad092. https://doi.org/10.1093/gigascience/giad092

### Acknowledgment

VIEWpoly project is supported by the USDA, National Institute of Food and Agriculture (NIFA), Specialty Crop Research Initiative (SCRI) project [‘‘Tools for Genomics-Assisted Breeding in Polyploids: Development of a Community Resource’’](https://www.polyploids.org/) and by the Bill & Melinda Gates Foundation under the Genetic Advances and [Innovative Seed Systems for Sweetpotato project (SweetGAINS)](https://cgspace.cgiar.org/handle/10568/106838).
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