phyloseq

name	phyloseq
description	phyloseq — Bioconductor R package for storing and analyzing microbiome census data (OTU/ASV tables, taxonomy, phylogeny, sample data) with ggplot2 graphics. Use as a data container and classic analysis API; many DA/network tools accept phyloseq objects. Upstream: https://github.com/joey711/phyloseq. Route via research-analysis; modular paper workflows also via microeco.
license	MIT
category	evaluation
tags	["phyloseq","Bioconductor","R","microbiome","diversity","visualization"]
upstream	https://github.com/joey711/phyloseq
stage	report

phyloseq

Upstream: joey711/phyloseq · Bioconductor: https://bioconductor.org/packages/phyloseq/

Citation

McMurdie, P. J. & Holmes, S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE 8, e61217 (2013). https://doi.org/10.1371/journal.pone.0061217

See also docs/references.md.

Analytical thinking

phyloseq is the long-standing R data class + plotting stack for microbiome tables. Use it to organize ASV/species × sample matrices with taxonomy and trees, then pass objects into ancombc, vegan ordinations, or custom ggplot2. For a more modular modern paper workflow, also consider microeco (can coexist).

Pin Bioconductor release. Avoid double rarefaction without stating rationale.

How to run

BiocManager::install("phyloseq")
library(phyloseq)
# ps <- phyloseq(otu_table(...), sample_data(...), tax_table(...), phy_tree(...))
# plot_bar / plot_ordination / transform_sample_counts — see vignettes

Decision tree

R microbiome data structure / classic plots?
├─ phyloseq object + ggplot2 → phyloseq
├─ Modular R6 paper workflow → microeco
├─ DA models → ancombc / maaslin2
└─ Networks → spieceasi / sparcc

Related skills

research-analysis · microeco · ancombc · maaslin2 · spieceasi · visualization · tool-selection