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ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization.

Chen Yang¹, Jiahao Mai¹, Xuan Cao²

¹Department of Biostatistics, Southern Medical University, Guangzhou 510515, China.

Bioinformatics (Oxford, England)

|August 1, 2023

Summary

This summary is machine-generated.

Researchers can now analyze microbiome functional pathways using the R package ggpicrust2. This tool enhances differential abundance analysis for 16S rRNA data, offering deeper functional insights into microbial communities.

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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

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Published on: July 1, 2020

Area of Science:

Microbiome research
Bioinformatics
Computational biology

Background:

Microbiome studies are shifting from composition to function.
Intestinal microbiome function impacts inflammation and immune responses.
16S rRNA sequencing provides composition but not direct functional gene information.

Purpose of the Study:

To introduce ggpicrust2, an R package for analyzing microbiome functional profiles.
To enable differential abundance testing of pathway abundances predicted from 16S rRNA data.
To provide researchers with a tool for in-depth functional analysis of microbial communities.

Main Methods:

Development of the ggpicrust2 R package.
Utilizes PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) for functional predictions.
Implements differential abundance analyses and creates visualizations.

Main Results:

ggpicrust2 enables extensive differential abundance analyses of predicted functional pathways.
The package generates visually appealing outputs to highlight functional signals.
Researchers can gain deeper insights into microbial community function.

Conclusions:

ggpicrust2 addresses the need for robust tools to analyze microbiome functional data.
The R package facilitates publishable research by providing advanced analytical capabilities.
ggpicrust2 enhances the interpretation of microbiome functional profiles derived from 16S rRNA sequencing.