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Related Concept Videos

Introduction to R01:11

Introduction to R

R is a powerful software environment for statistical computing and graphics. Originating as an implementation of the S language, developed at Bell Laboratories, R has evolved into a robust, open-source statistical software favored by statisticians and data scientists worldwide. Its comprehensive suite includes data manipulation, calculation, and graphical display capabilities, making it versatile for data analysis and visualization. Its programming language is at the core of R's functionality,...
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R chart, or range chart, is a fundamental tool in statistical process control used to monitor the variability within a process. It complements the X-bar (x̄) chart by focusing on the range of the data, rather than individual values, providing a clear picture of the process dispersion over time.
An R chart plots the range of subsets of measurements collected from a process. Each point on the chart represents the range—defined as the difference between the maximum and minimum values—of a sample...

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MetaDAVis: An R shiny application for metagenomic data analysis and visualization.

Sankarasubramanian Jagadesan1, Chittibabu Guda1,2

  • 1Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.

Plos One
|April 7, 2025
PubMed
Summary
This summary is machine-generated.

We developed MetaDAVis, an R Shiny tool for analyzing and visualizing human microbiome sequencing data. This user-friendly application simplifies complex metagenomic data interpretation for researchers without programming experience.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • The human microbiome is crucial for health and disease.
  • High-throughput sequencing generates vast amounts of microbiome data.
  • Analyzing and visualizing this data presents significant challenges for biological interpretation.

Purpose of the Study:

  • To develop an interactive tool for metagenome data analysis and visualization.
  • To address the challenges of interpreting large-scale microbiome sequencing data.
  • To provide a user-friendly platform for both 16S rRNA and whole genome sequencing data.

Main Methods:

  • Developed an R Shiny application named MetaDAVis.
  • Integrated six core analysis modules: taxonomic abundance, diversity, dimension reduction (PCA, t-SNE, UMAP), correlation, heatmap generation, and differential abundance.
  • Ensured the tool is interactive, dynamic, and customizable.

Main Results:

  • MetaDAVis enables comprehensive analysis and visualization of microbiome data.
  • The tool generates interactive figures and tables for easier data understanding.
  • It supports both standalone and web-based interfaces, catering to users with and without programming backgrounds.

Conclusions:

  • MetaDAVis offers a powerful, accessible solution for metagenomic data analysis and visualization.
  • The tool empowers researchers to derive meaningful biological insights from complex microbiome datasets.
  • Its user-friendly design democratizes advanced bioinformatics analysis for a wider scientific audience.