Package: tidypq 0.1.1

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]

tidypq_0.1.1.tar.gz
tidypq_0.1.1.zip(r-4.7)tidypq_0.1.1.zip(r-4.6)tidypq_0.1.1.zip(r-4.5)
tidypq_0.1.1.tgz(r-4.6-any)tidypq_0.1.1.tgz(r-4.5-any)
tidypq_0.1.1.tar.gz(r-4.7-any)tidypq_0.1.1.tar.gz(r-4.6-any)
tidypq_0.1.1.tgz(r-4.6-emscripten)
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:

4.29 score 1 stars 13 scripts 27 exports 126 dependencies

Last updated from:71930f3e2c. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR369
source / vignettesOK356
linux-release-x86_64ERROR339
macos-release-arm64ERROR271
macos-oldrel-arm64ERROR194
windows-develERROR288
windows-releaseERROR265
windows-oldrelERROR316
wasm-releaseOK174

Exports:arrange_samples_pqarrange_taxa_pqchimera_removal_dada2chimera_removal_vs_refcontam_blocklist_pqcontam_corr_pqcreate_chimera_pqdecontam_sam_controldecontam_taxa_controlfilter_occurrences_pqfilter_samples_pqfilter_taxa_pqfilter_tree_pqknown_contaminant_generamutate_occurrences_pqmutate_samdata_pqmutate_taxa_pqneg_control_classify_pqneg_control_clean_pqneg_control_diag_pqrename_samples_pqrename_taxa_pqselect_samdata_pqselect_taxa_pqslice_samples_pqslice_taxa_pqtaxa_prevalence

Dependencies:abindade4alphahullapeBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitopscigarillocliclustercodetoolscpp11crayoncubaturedada2data.tabledbmssDelayedArraydeldirdigestdiventdoFuturedplyrEntropyEstimationfarverforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicAlignmentsGenomicRangesggplot2globalsgluegoftestgtablehwriterigraphinterpIRangesisobanditeratorsjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvMiscMetabarmulttestnlmeparallellypatchworkpermutephyloseqpillarpixmappkgconfigplyrpngpolyclipprogressrpurrrpwalignR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorsS7scalesSeqinfosgeostatShortReadsnowspSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilssplancsstringistringrSummarizedExperimentsurvivaltensortibbletidyrtidyselectutf8vctrsveganviridisLitewithrXVector

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

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: 2026-05-06
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
Remove chimeric sequences using dada2chimera_removal_dada2
Remove chimeric sequences using vsearch and a reference databasechimera_removal_vs_ref
Flag taxa whose genus belongs to a known-contaminant blocklistcontam_blocklist_pq
Detect contaminants by correlating taxon reads with total sample depthcontam_corr_pq
Create a phyloseq object with synthetic chimeric sequencescreate_chimera_pq
Decontaminate based on negative/blank control samplesdecontam_sam_control
Decontaminate based on control taxadecontam_taxa_control
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
Known reagent- and laboratory-contaminant generaknown_contaminant_genera
Transform OTU table valuesmutate_occurrences_pq
Add or modify columns in sample_datamutate_samdata_pq
Add or modify columns in tax_tablemutate_taxa_pq
Classify taxa found in negative controls into contamination categoriesneg_control_classify_pq
Remove negative-control contaminants from a phyloseq objectneg_control_clean_pq
Diagnose contamination from negative controlsneg_control_diag_pq
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
Calculate taxa prevalencetaxa_prevalence