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bioRxiv · 10.1101/2023.11.29.569321

MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics

Ma, K.·Thairu, M. W.·Sankaran, K.
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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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Ma, K., Thairu, M. W., Sankaran, K.. 2023-11-30. MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics. https://doi.org/10.1101/2023.11.29.569321

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