ShinySperm: navigating the sperm proteome landscape
David A. Skerrett-Byrne![https://orcid.org/0000-0002-1804-1826](/media/client/orcid_16x16.png)
![https://orcid.org/0000-0001-8815-1409](/media/client/orcid_16x16.png)
![https://orcid.org/0000-0003-2745-8188](/media/client/orcid_16x16.png)
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Abstract
Integrated omics studies hold a crucial role in improving our understanding of reproductive biology. However, the complex datasets so generated are often only accessible via supplementary data files, which lack the capacity for interactive features to allow users to readily interrogate and visualise data of interest.
The intent of this technical note was to develop an interactive web-based application that enables detailed interrogation of a representative sperm proteome, facilitating a deeper understanding of the proteins identified, their relative abundance, classifications, functions, and associated phenotypes.
We developed a Shiny web application, ShinySperm (https://reproproteomics.shinyapps.io/ShinySperm/), utilising R and several complementary libraries for data manipulation (dplyr), interactive tables (DT), and visualisation (ggplot2, plotly). ShinySperm features a responsive user interface, dynamic filtering options, interactive charts, and data export capabilities.
ShinySperm allows users to interactively search, filter, and visualise sperm proteomics data based on key features (e.g. protein classification, sperm cell domain, presence, or absence at different maturation stages). This application responds live to filtering options and enables the generation of interactive plots and tables, thus enhancing user engagement and understanding of the data.
ShinySperm provides a robust platform for the dynamic exploration of epididymal sperm proteome data. It significantly improves accessibility and interpretability of complex datasets, allowing for effective data-driven insights.
This technical note highlights the potential of interactive web applications in reproductive biology and provides a plug and play script for the field to produce applications for meaningful researcher interaction with complex omic datasets.
Keywords: epididymis, fertility, male fertility, proteomics, publicly accessible data, ShinySperm app, sperm, sperm maturation, sperm proteome.
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