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ShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studies

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dc.contributor.authorHussain, Waseemen
dc.contributor.authorCampbell, Malachy T.en
dc.contributor.authorWalia, Harkamalen
dc.contributor.authorMorota, Gotaen
dc.date.accessioned2021-10-20T11:49:53Zen
dc.date.available2021-10-20T11:49:53Zen
dc.date.issued2018-10-01en
dc.date.updated2021-10-20T11:49:50Zen
dc.description.abstractOwning to advancements in sensor-based, non-destructive phenotyping platforms, researchers are increasingly collecting data with higher temporal resolution. These phenotypes collected over several time points are cataloged as longitudinal traits and used for genome-wide association studies (GWAS). Longitudinal GWAS typically yield a large number of output files, posing a significant challenge to data interpretation and visualization. Efficient, dynamic, and integrative data visualization tools are essential for the interpretation of longitudinal GWAS results for biologists; however, these tools are not widely available to the community. We have developed a flexible and user-friendly Shiny-based online application, ShinyAIM, to dynamically view and interpret temporal GWAS results. The main features of the application include (a) interactive Manhattan plots for single time points, (b) a grid plot to view Manhattan plots for all time points simultaneously, (c) dynamic scatter plots for p-value-filtered selected markers to investigate co-localized genomic regions across time points, (d) and interactive phenotypic data visualization to capture variation and trends in phenotypes. The application is written entirely in the R language and can be used with limited programming experience. ShinyAIM is deployed online as a Shiny web server application at https://chikudaisei.shinyapps.io/shinyaim/, enabling easy access for users without installation. The application can also be launched on a local machine in RStudio.en
dc.description.versionPublished versionen
dc.format.extent4 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifierARTN 91 (Article number)en
dc.identifier.doihttps://doi.org/10.1002/pld3.91en
dc.identifier.eissn2475-4455en
dc.identifier.issn2475-4455en
dc.identifier.issue10en
dc.identifier.orcidMorota, Gota [0000-0002-3567-6911]en
dc.identifier.otherPLD391 (PII)en
dc.identifier.pmid31245691en
dc.identifier.urihttp://hdl.handle.net/10919/105420en
dc.identifier.volume2en
dc.language.isoenen
dc.publisherWileyen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000509895400001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectLife Sciences & Biomedicineen
dc.subjectPlant Sciencesen
dc.subjectgenome-wide association studiesen
dc.subjectinteractive visualizationen
dc.subjectlongitudinal traitsen
dc.subjectShinyAIMen
dc.subjectgenome‐wide association studiesen
dc.titleShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studiesen
dc.title.serialPlant Directen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2018-10-08en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Animal and Poultry Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen

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