microeco 2: A comprehensive R package for downstream analysis of microbiome omics data

Area of Science:

• Bioinformatics
• Computational Biology
• Microbiome Research

Background:

• Efficient downstream analysis of microbiome data is a significant challenge.
• The R microeco package, initially released in 2020, is widely used for omics data analysis.
• Version 2.0 represents a substantial upgrade to the microeco package.

Purpose of the Study:

• To detail the extensive updates and enhancements in the second version of the R microeco package.
• To highlight the expanded functionalities for microbiome and other omics data analysis.
• To showcase the improved capabilities for statistical analysis and visualization.

Main Methods:

• Addition of new classes for data normalization and machine learning.
• Incorporation of additional analytical methods and functions.
• Optimization of the parameter system for broader applicability.
• Code restructuring for better integration of analysis and visualization.
• Extension of functions for complex abundance data from metagenomic/metatranscriptomic analyses.
• Inclusion of methods common in transcriptomic and metabolomic data analysis.

Main Results:

• Microeco package 2.0 offers broader method coverage and wider application scenarios than previous versions and other R packages.
• The package supports complex data formats from metagenomic and metatranscriptomic analyses.
• New functionalities enhance the analysis of microbiome, transcriptomic, and metabolomic data.

Conclusions:

• The microeco package 2.0 provides a more comprehensive and versatile tool for omics data analysis.
• Its active user base and open-source availability facilitate widespread adoption.
• The package is a valuable resource for researchers in microbiome and related fields.