microbiome

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 1.34.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: phyloseq, ggplot2
• Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, tibble, tidyr, vegan
• Install: BiocManager::install("microbiome")

When to Use

• Facilitating phyloseq-based exploration and analysis of taxonomic profiling data.
• Performing manipulation, statistical analysis, and visualization of taxonomic profiling data.
• Standardizing analyses and developing best practices for targeted microbiome analysis.

When NOT to Use

• For new projects or multi-omics data analysis, use the miaverse project instead, as microbiome development has been discontinued.
• For workflows based on the new TreeSummarizedExperiment data container, use miaverse packages instead of microbiome.

Data Requirements

• Taxonomic profiling data in the independent phyloseq data format.

Key Parameters

• No parameters are explicitly detailed in the provided vignette text.

Best Practices

• Transition to the miaverse project and TreeSummarizedExperiment data container for added capabilities in multi-omics data analysis.
• Use the package to facilitate scalable exploration of population cohorts and targeted case-control studies.
• Rely on the independent phyloseq package and data structures for R-based microbiome analysis.