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Related Concept Videos

Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...

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

Kaiyan Ma, Margaret W Thairu, Kris Sankaran

    Biorxiv : the Preprint Server for Biology
    |December 11, 2023
    PubMed
    Summary
    This summary is machine-generated.

    MolPad is a user-friendly R-Shiny dashboard for exploring longitudinal molecular co-expression in microbiomics. It visualizes complex relationships using networks and interactive plots, aiding microbiome data analysis.

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    Area of Science:

    • Microbiology
    • Bioinformatics
    • Data Science

    Background:

    • Understanding longitudinal molecular co-expression in microbiomics is crucial for deciphering microbial community dynamics.
    • Existing tools may lack user-friendliness or interactive visualization capabilities for complex co-expression patterns.

    Approach:

    • Developed MolPad, an R-Shiny package offering an interactive dashboard for microbiomics data.
    • Employs a focus-plus-context strategy, utilizing network visualizations to identify major co-expression patterns.
    • Integrates multiple plots (network, bar, line) and tables for comprehensive data exploration, with automated links to curated annotations.

    Key Points:

    • MolPad facilitates the overview of major co-expression patterns through network analysis.
    • The dashboard allows users to zoom into specific clusters of interest for detailed investigation.
    • Includes functions for data processing, making it accessible for users with limited R programming experience.

    Conclusions:

    • MolPad provides an effective and interactive platform for analyzing longitudinal molecular co-expression in microbiomics.
    • The package simplifies the exploration of complex microbial community dynamics, demonstrated through a cheese microbiome case study.