Package index

Sample-scale verbs

Filter, select, mutate, slice, arrange, and rename samples.

filter_samples_pq()

Filter samples in a phyloseq object

select_samdata_pq()

Select columns from sample_data in a phyloseq object

mutate_samdata_pq()

Add or modify columns in sample_data

slice_samples_pq()

Subset samples by position

arrange_samples_pq()

Arrange samples by column values

rename_samples_pq()

Rename columns in sample_data

Taxa-scale verbs

Filter, select, mutate, slice, arrange, and rename taxa.

filter_taxa_pq()

Filter taxa in a phyloseq object

select_taxa_pq()

Select columns from tax_table in a phyloseq object

mutate_taxa_pq()

Add or modify columns in tax_table

slice_taxa_pq()

Subset taxa by position

arrange_taxa_pq()

Arrange taxa by column values

rename_taxa_pq()

Rename columns in tax_table

Occurrence-scale verbs

Filter and transform OTU table values.

filter_occurrences_pq()

Filter occurrences in the OTU table

mutate_occurrences_pq()

Transform OTU table values

Tree-scale verbs

Filter phylogenetic trees.

filter_tree_pq()

Filter phyloseq by tree topology

Tidy conversion

Convert a phyloseq object into a tidy tibble.

pq_to_tidy()

Convert a phyloseq object to a tidy tibble

tax_table_to_df()

Convert a tax_table into a data.frame with numeric and list columns

Merging markers

Stack phyloseq objects from different markers into one object.

merge_markers_pq()

Merge phyloseq objects from different markers into a single object

Helpers

Utility functions for common operations.

taxa_prevalence()

Calculate taxa prevalence

Contaminant detectors

Flag suspect taxa; each returns a contam_tbl consumed by filter_contam_pq().

identify_contam_blocklist_pq()

Detect taxa whose genus belongs to a known-contaminant blocklist

identify_contam_chimera_pq()

Detect chimeric taxa with dada2 or vsearch

identify_contam_corr_pq()

Detect contaminants by correlating taxon reads with total sample depth

identify_contam_negcontrol_pq()

Detect contaminants from negative-control occurrence patterns

identify_contam_primer_pq()

Detect taxa whose representative sequence contains a primer

known_contaminant_genera()

Known reagent- and laboratory-contaminant genera

Contaminant removal and the contam_tbl object

Remove flagged taxa and work with the detector output object.

filter_contam_pq()

Remove contaminant taxa flagged by a detector

filter_chimera_pq()

Remove chimeric taxa in one step

new_contam_tbl() is_contam_tbl()

The contam_tbl class

print(<contam_tbl>)

Print a contam_tbl

rbind(<contam_tbl>)

Combine several contam_tbl objects

autoplot(<contam_tbl>) plot(<contam_tbl>)

Diagnostic plot for a contam_tbl

Control-based decontamination

Zero out occurrences below a background level estimated from control samples or control taxa.

decontam_control_samples_pq()

Decontaminate based on negative/blank control samples

decontam_control_taxa_pq()

Decontaminate based on control taxa

Cross-talk (tag-jump) filtering

Detect, visualise, and remove per-cell cross-talk (tag-switching) with the UNCROSS2 score.

uncross2_pq()

Remove cross-talk (tag-jumps) using the UNCROSS2 score

plot_uncross2_scores()

Plot UNCROSS2 cross-talk scores against OTU abundance

Chimera utilities

Generate synthetic chimeras for benchmarking detectors.

create_chimera_pq()

Create a phyloseq object with synthetic chimeric sequences