| 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)
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
