AI Article Synopsis
- The R-Shiny package MolPad offers an interactive dashboard for analyzing longitudinal molecular co-expression in microbiomics through network overviews and focused cluster analysis.
- It features a user-friendly design, automatically linking to curated online annotations while providing visualizations such as cluster networks, taxonomic bar plots, line plots of data modalities, and pathway tables.
- The package is accessible for beginners in R, demonstrated with a case study on metagenomics in cheese microbiome analysis.
Article Abstract
The R-Shiny package MolPad provides an interactive dashboard for understanding the dynamics of longitudinal molecular co-expression in microbiomics. The main idea for addressing the issue is first to use a network to overview major patterns among their predictive relationships and then zoom into specific clusters of interest. It is designed with a focus-plus-context analysis strategy and automatically generates links to online curated annotations. The dashboard consists of a cluster-level network, a bar plot of taxonomic composition, a line plot of data modalities, and a table for each pathway. Further, the package includes functions that handle the data processing for creating the dashboard. This makes it beginner-friendly for users with less R programming experience. We illustrate these methods with a case study on a longitudinal metagenomics analysis of the cheese microbiome.
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Source |
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10705384 | PMC |
| http://dx.doi.org/10.1101/2023.11.29.569321 | DOI Listing |
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