PT  - JOURNAL ARTICLE
AU  - Waseem Hussain
AU  - Malachy Campbell
AU  - Harkamal Walia
AU  - Gota Morota
TI  - ShinyAIM: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies
AID  - 10.1101/383026
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 383026
4099  - http://biorxiv.org/content/early/2018/08/02/383026.short
4100  - http://biorxiv.org/content/early/2018/08/02/383026.full
AB  - Abstract Due 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 for data interpretation and visualization. Efficient, dynamic, and integrative data visualization tools are essential for the interpretation of longitudinal GWAS results for biologists but 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 (i) interactive Manhattan plots for single time points, (ii) grid plot to view Manhattan plots for all time points simultaneously, (iii) dynamic scatter plots for p-value-filtered selected markers to investigate co-localized genomic regions across time points, (iv) 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.