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    "arrange_taxa_pq",
    "create_chimera_pq",
    "decontam_control_samples_pq",
    "decontam_control_taxa_pq",
    "filter_chimera_pq",
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    "filter_samples_pq",
    "filter_taxa_pq",
    "filter_tree_pq",
    "identify_contam_blocklist_pq",
    "identify_contam_chimera_pq",
    "identify_contam_corr_pq",
    "identify_contam_negcontrol_pq",
    "identify_contam_primer_pq",
    "is_contam_tbl",
    "known_contaminant_genera",
    "merge_markers_pq",
    "mutate_occurrences_pq",
    "mutate_samdata_pq",
    "mutate_taxa_pq",
    "new_contam_tbl",
    "plot_uncross2_scores",
    "pq_to_tidy",
    "rename_samples_pq",
    "rename_taxa_pq",
    "select_samdata_pq",
    "select_taxa_pq",
    "slice_samples_pq",
    "slice_taxa_pq",
    "tax_table_to_df",
    "taxa_prevalence",
    "uncross2_pq"
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    {
      "page": "arrange_samples_pq",
      "title": "Arrange samples by column values",
      "topics": [
        "arrange_samples_pq"
      ]
    },
    {
      "page": "arrange_taxa_pq",
      "title": "Arrange taxa by column values",
      "topics": [
        "arrange_taxa_pq"
      ]
    },
    {
      "page": "autoplot.contam_tbl",
      "title": "Diagnostic plot for a 'contam_tbl'",
      "topics": [
        "autoplot.contam_tbl",
        "plot.contam_tbl"
      ]
    },
    {
      "page": "create_chimera_pq",
      "title": "Create a phyloseq object with synthetic chimeric sequences",
      "topics": [
        "create_chimera_pq"
      ]
    },
    {
      "page": "decontam_control_samples_pq",
      "title": "Decontaminate based on negative/blank control samples",
      "topics": [
        "decontam_control_samples_pq"
      ]
    },
    {
      "page": "decontam_control_taxa_pq",
      "title": "Decontaminate based on control taxa",
      "topics": [
        "decontam_control_taxa_pq"
      ]
    },
    {
      "page": "filter_chimera_pq",
      "title": "Remove chimeric taxa in one step",
      "topics": [
        "filter_chimera_pq"
      ]
    },
    {
      "page": "filter_contam_pq",
      "title": "Remove contaminant taxa flagged by a detector",
      "topics": [
        "filter_contam_pq"
      ]
    },
    {
      "page": "filter_occurrences_pq",
      "title": "Filter occurrences in the OTU table",
      "topics": [
        "filter_occurrences_pq"
      ]
    },
    {
      "page": "filter_samples_pq",
      "title": "Filter samples in a phyloseq object",
      "topics": [
        "filter_samples_pq"
      ]
    },
    {
      "page": "filter_taxa_pq",
      "title": "Filter taxa in a phyloseq object",
      "topics": [
        "filter_taxa_pq"
      ]
    },
    {
      "page": "filter_tree_pq",
      "title": "Filter phyloseq by tree topology",
      "topics": [
        "filter_tree_pq"
      ]
    },
    {
      "page": "identify_contam_blocklist_pq",
      "title": "Detect taxa whose genus belongs to a known-contaminant blocklist",
      "topics": [
        "identify_contam_blocklist_pq"
      ]
    },
    {
      "page": "identify_contam_chimera_pq",
      "title": "Detect chimeric taxa with dada2 or vsearch",
      "topics": [
        "identify_contam_chimera_pq"
      ]
    },
    {
      "page": "identify_contam_corr_pq",
      "title": "Detect contaminants by correlating taxon reads with total sample depth",
      "topics": [
        "identify_contam_corr_pq"
      ]
    },
    {
      "page": "identify_contam_negcontrol_pq",
      "title": "Detect contaminants from negative-control occurrence patterns",
      "topics": [
        "identify_contam_negcontrol_pq"
      ]
    },
    {
      "page": "identify_contam_primer_pq",
      "title": "Detect taxa whose representative sequence contains a primer",
      "topics": [
        "identify_contam_primer_pq"
      ]
    },
    {
      "page": "known_contaminant_genera",
      "title": "Known reagent- and laboratory-contaminant genera",
      "topics": [
        "known_contaminant_genera"
      ]
    },
    {
      "page": "merge_markers_pq",
      "title": "Merge phyloseq objects from different markers into a single object",
      "topics": [
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    },
    {
      "page": "mutate_occurrences_pq",
      "title": "Transform OTU table values",
      "topics": [
        "mutate_occurrences_pq"
      ]
    },
    {
      "page": "mutate_samdata_pq",
      "title": "Add or modify columns in sample_data",
      "topics": [
        "mutate_samdata_pq"
      ]
    },
    {
      "page": "mutate_taxa_pq",
      "title": "Add or modify columns in tax_table",
      "topics": [
        "mutate_taxa_pq"
      ]
    },
    {
      "page": "plot_uncross2_scores",
      "title": "Plot UNCROSS2 cross-talk scores against OTU abundance",
      "topics": [
        "plot_uncross2_scores"
      ]
    },
    {
      "page": "pq_to_tidy",
      "title": "Convert a phyloseq object to a tidy tibble",
      "topics": [
        "pq_to_tidy"
      ]
    },
    {
      "page": "print.contam_tbl",
      "title": "Print a 'contam_tbl'",
      "topics": [
        "print.contam_tbl"
      ]
    },
    {
      "page": "rbind.contam_tbl",
      "title": "Combine several 'contam_tbl' objects",
      "topics": [
        "rbind.contam_tbl"
      ]
    },
    {
      "page": "rename_samples_pq",
      "title": "Rename columns in sample_data",
      "topics": [
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      ]
    },
    {
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      "title": "Rename columns in tax_table",
      "topics": [
        "rename_taxa_pq"
      ]
    },
    {
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      "title": "Select columns from sample_data in a phyloseq object",
      "topics": [
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    },
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      "title": "Subset samples by position",
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      "topics": [
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      "title": "Convert a 'tax_table' into a data.frame with numeric and list columns",
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      ]
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    {
      "page": "taxa_prevalence",
      "title": "Calculate taxa prevalence",
      "topics": [
        "taxa_prevalence"
      ]
    },
    {
      "page": "uncross2_pq",
      "title": "Remove cross-talk (tag-jumps) using the UNCROSS2 score",
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