Package index

All functions

arrange_samples_pq()

Arrange samples by column values

arrange_taxa_pq()

Arrange taxa by column values

chimera_removal_dada2()

Remove chimeric sequences using dada2

create_chimera_pq()

Create a phyloseq object with synthetic chimeric sequences

decontam_sam_control()

Decontaminate based on negative/blank control samples

decontam_taxa_control()

Decontaminate based on control taxa

filter_occurrences_pq()

Filter occurrences in the OTU table

filter_samples_pq()

Filter samples in a phyloseq object

filter_taxa_pq()

Filter taxa in a phyloseq object

filter_tree_pq()

Filter phyloseq by tree topology

mutate_occurrences_pq()

Transform OTU table values

mutate_samdata_pq()

Add or modify columns in sample_data

mutate_taxa_pq()

Add or modify columns in tax_table

plot_sample_depth_pq()

Plot sample depth differences to detect outliers

rename_samples_pq()

Rename columns in sample_data

rename_taxa_pq()

Rename columns in tax_table

select_samdata_pq()

Select columns from sample_data in a phyloseq object

select_taxa_pq()

Select columns from tax_table in a phyloseq object

slice_samples_pq()

Subset samples by position

slice_taxa_pq()

Subset taxa by position

taxa_prevalence()

Calculate taxa prevalence