bioconductor-microbiome

name	bioconductor-microbiome
description	Utilities for microbiome analysis.
when_to_use	Use when: 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.. Not for: 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.
user-invocable	false

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.

Common Pitfalls

• Using discontinued software for new multi-omics projects: The microbiome package development is discontinued. Fix: Shift to miaverse tools based on TreeSummarizedExperiment.
• Incompatibility with new data containers: Attempting to use TreeSummarizedExperiment objects directly in microbiome. Fix: Use phyloseq format or migrate to miaverse.
• Missing general-purpose tools: Relying solely on microbiome for all analyses. Fix: Integrate with the independent phyloseq package and its data structures.

Alternatives

• phyloseq: The independent package and data structure for R-based microbiome analysis that microbiome relies heavily upon.
• miaverse: The recommended successor project based on the TreeSummarizedExperiment data container.

Citations

• Leo Lahti et al. (Bioconductor, 2017-2020). Tools for microbiome analysis in R. Microbiome package version.

References

• Homepage: https://bioconductor.org/packages/microbiome
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/microbiome

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