Package: tidypq 0.3.0.9000

tidypq: Tidyverse-Style Verbs for 'phyloseq' Objects

Tidyverse-style verbs for manipulating 'phyloseq' objects at four scales: samples, taxa, occurrences, and tree. Functions follow a consistent naming convention and support data masking for intuitive filtering, selection, and mutation operations. Designed for metabarcoding analyses, it integrates with 'MiscMetabar' and the 'pqverse' ecosystem.

Authors:Adrien Taudière [aut, cre, cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tidypq/json (API)

# Install 'tidypq' in R:
install.packages('tidypq', repos = c('https://adrientaudiere.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adrientaudiere/tidypq/issues

Pkgdown/docs site:https://adrientaudiere.github.io

On CRAN:

Conda:

4.65 score 1 stars 15 scripts 34 exports 119 dependencies

Last updated from:9fe55631b1. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR304
source / vignettesOK313
linux-releaseERROR274
macos-releaseERROR259
macos-oldrelERROR189
windows-develERROR241
windows-releaseERROR191
windows-oldrelERROR258
wasm-releaseOK149

Exports:arrange_samples_pqarrange_taxa_pqcreate_chimera_pqdecontam_control_samples_pqdecontam_control_taxa_pqfilter_chimera_pqfilter_contam_pqfilter_occurrences_pqfilter_samples_pqfilter_taxa_pqfilter_tree_pqidentify_contam_blocklist_pqidentify_contam_chimera_pqidentify_contam_corr_pqidentify_contam_negcontrol_pqidentify_contam_primer_pqis_contam_tblknown_contaminant_generamerge_markers_pqmutate_occurrences_pqmutate_samdata_pqmutate_taxa_pqnew_contam_tblplot_uncross2_scorespq_to_tidyrename_samples_pqrename_taxa_pqselect_samdata_pqselect_taxa_pqslice_samples_pqslice_taxa_pqtax_table_to_dftaxa_prevalenceuncross2_pq

Dependencies:abindade4alphahullapeBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitopscigarillocliclustercodetoolscpp11crayoncubaturedada2data.tabledbmssdeldirdigestdiventdoFuturedplyrEntropyEstimationfarverforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicAlignmentsGenomicRangesggplot2globalsgluegoftestgtablehwriterigraphinterpIRangesisobanditeratorsjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclelistenvmagrittrMASSMatrixmgcvMiscMetabarmulttestnlmeparallellypermutephyloseqpillarpixmappkgconfigplyrpngpolyclipprogressrpurrrpwalignR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreshape2RhtslibrlangRsamtoolsS4VectorsS7scalesSeqinfosgeostatShortReadsnowspspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilssplancsstringistringrsurvivaltensortibbletidyrtidyselectutf8vctrsveganviridisLitewithrXVector

Benchmarking Chimera Detection Methods
Overview | Data Preparation | Creating Test Data with Synthetic Chimeras | Comparing Detection Methods | Helper function for benchmarking | Run benchmarks | Benchmark Summary Table | Analyzing Missed Chimeras | Comparing Detection Across Different Chimera Types | Summary Table: All Scenarios | Visualizing Results | Effect of Chimera Abundance on Detection | Abundance Summary Table | Visualizing Abundance Effect | Effect of Parent Sequence Distance
Rendered fromchimera_detection_testing.Rmdusingknitr::rmarkdown

Last update: 2026-06-26
Started: 2026-03-06

Detecting and removing contaminants
The detect-then-filter design | A first detector | Removing flagged taxa | Combining detectors | Diagnostics | Negative-control classification | Abundance-, sequence-, and chimera-based detectors | Control-based decontamination (a different tool)
Rendered fromdecontamination.Rmdusingknitr::rmarkdown

Last update: 2026-06-26
Started: 2026-06-26

Advanced Usage
Custom functions in filter | Custom functions in mutate | Occurrence-level transformations | Complex pipelines
Rendered fromadvanced-usage.Rmdusingknitr::rmarkdown

Last update: 2026-05-06
Started: 2026-03-06

Getting Started with tidypq
Overview | Filter samples | Filter taxa | Mutate | Select columns | Chaining operations
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-05-06
Started: 2026-03-06

Readme and manuals

Help Manual

Help pageTopics
Arrange samples by column valuesarrange_samples_pq
Arrange taxa by column valuesarrange_taxa_pq
Diagnostic plot for a 'contam_tbl'autoplot.contam_tbl plot.contam_tbl
Create a phyloseq object with synthetic chimeric sequencescreate_chimera_pq
Decontaminate based on negative/blank control samplesdecontam_control_samples_pq
Decontaminate based on control taxadecontam_control_taxa_pq
Remove chimeric taxa in one stepfilter_chimera_pq
Remove contaminant taxa flagged by a detectorfilter_contam_pq
Filter occurrences in the OTU tablefilter_occurrences_pq
Filter samples in a phyloseq objectfilter_samples_pq
Filter taxa in a phyloseq objectfilter_taxa_pq
Filter phyloseq by tree topologyfilter_tree_pq
Detect taxa whose genus belongs to a known-contaminant blocklistidentify_contam_blocklist_pq
Detect chimeric taxa with dada2 or vsearchidentify_contam_chimera_pq
Detect contaminants by correlating taxon reads with total sample depthidentify_contam_corr_pq
Detect contaminants from negative-control occurrence patternsidentify_contam_negcontrol_pq
Detect taxa whose representative sequence contains a primeridentify_contam_primer_pq
Known reagent- and laboratory-contaminant generaknown_contaminant_genera
Merge phyloseq objects from different markers into a single objectmerge_markers_pq
Transform OTU table valuesmutate_occurrences_pq
Add or modify columns in sample_datamutate_samdata_pq
Add or modify columns in tax_tablemutate_taxa_pq
Plot UNCROSS2 cross-talk scores against OTU abundanceplot_uncross2_scores
Convert a phyloseq object to a tidy tibblepq_to_tidy
Print a 'contam_tbl'print.contam_tbl
Combine several 'contam_tbl' objectsrbind.contam_tbl
Rename columns in sample_datarename_samples_pq
Rename columns in tax_tablerename_taxa_pq
Select columns from sample_data in a phyloseq objectselect_samdata_pq
Select columns from tax_table in a phyloseq objectselect_taxa_pq
Subset samples by positionslice_samples_pq
Subset taxa by positionslice_taxa_pq
Convert a 'tax_table' into a data.frame with numeric and list columnstax_table_to_df
Calculate taxa prevalencetaxa_prevalence
Remove cross-talk (tag-jumps) using the UNCROSS2 scoreuncross2_pq