pqverse

The pqverse is a set of R packages for metabarcoding analysis that share the phyloseq object as their central data structure. Installing and loading pqverse attaches all member packages in a single step, much like the tidyverse.

Installation

You can install pqverse from GitHub:

# install.packages("pak")
pak::pak("adrientaudiere/pqverse")

Usage

library(pqverse)
#> ── Attaching pqverse packages ──────────────────────────────────
#> ✔ MiscMetabar 0.14.6
#> ✔ tidypq      0.1.0
#> ✔ comparpq    0.1.0
#> ✔ taxinfo     0.1.2
#> ✔ greenAlgoR  0.1.2
#> ✔ dbpq        0.0.0.9000

Packages

Package	Description	Links
MiscMetabar	Miscellaneous functions for description, transformation, exploration, and reproducibility of metabarcoding analyses. Built on phyloseq, dada2, and targets.	CRAN, JOSS
tidypq	Tidyverse-style verbs for manipulating phyloseq objects at four scales: samples, taxa, occurrences, and tree.
comparpq	Tools to compare and analyse multiple phyloseq objects.	Website
taxinfo	Augment phyloseq objects with taxonomy-based information from GBIF, Wikipedia, and GloBI.	Website
greenAlgoR	Carbon footprint estimation for R computations, based on the Green Algorithms framework.	Website
dbpq	Management of taxonomic reference database	Website

Utilities

# List all pqverse packages
pqverse_packages()

# Check installed versions
pqverse_update()