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  "Title": "Miscellaneous Functions for Metabarcoding Analysis",
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  "Authors@R": "person(\"Adrien\", \"Taudière\", email = \"adrien.taudiere@zaclys.net\",\nrole = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0003-1088-1182\"))",
  "Description": "Facilitate the description, transformation, exploration,\nand reproducibility of metabarcoding analyses. 'MiscMetabar' is\nmainly built on top of the 'phyloseq', 'dada2' and 'targets' R\npackages. It helps to build reproducible and robust\nbioinformatics pipelines in R. 'MiscMetabar' makes ecological\nanalysis of alpha and beta-diversity easier, more reproducible\nand more powerful by integrating a large number of tools.\nImportant features are described in Taudière A. (2023)\n<doi:10.21105/joss.06038>.",
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    "add_funguild_info",
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    "all_object_size",
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    "assign_blastn",
    "assign_dada2",
    "assign_idtaxa",
    "assign_sintax",
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    "asv2otu",
    "biplot_physeq",
    "biplot_pq",
    "blast_pq",
    "blast_to_derep",
    "blast_to_phyloseq",
    "build_phytree_pq",
    "chimera_detection_vs",
    "chimera_removal_vs",
    "circle_pq",
    "clean_physeq",
    "clean_pq",
    "compare_pairs_pq",
    "count_seq",
    "cutadapt_remove_primers",
    "diff_fct_diff_class",
    "dist_bycol",
    "dist_pos_control",
    "distri_1_taxa",
    "fac2col",
    "filt_taxa_pq",
    "filt_taxa_wo_NA",
    "filter_asv_blast",
    "filter_taxa_blast",
    "filter_trim",
    "format2dada2",
    "format2dada2_species",
    "format2sintax",
    "formattable_pq",
    "funguild_assign",
    "funky_color",
    "get_file_extension",
    "get_funguild_db",
    "ggaluv_pq",
    "ggbetween_pq",
    "ggscatt_pq",
    "ggVenn_phyloseq",
    "ggvenn_pq",
    "glmutli_pq",
    "graph_test_pq",
    "hill_curves_pq",
    "hill_phyloseq",
    "hill_pq",
    "hill_test_rarperm_pq",
    "hill_tuckey_phyloseq",
    "hill_tuckey_pq",
    "iNEXT_pq",
    "is_cutadapt_installed",
    "is_falco_installed",
    "is_krona_installed",
    "is_mumu_installed",
    "is_swarm_installed",
    "is_vsearch_installed",
    "krona",
    "LCBD_pq",
    "learn_idtaxa",
    "list_fastq_files",
    "lulu",
    "lulu_phyloseq",
    "lulu_pq",
    "merge_krona",
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    "merge_taxa_vec",
    "multi_biplot_pq",
    "multipatt_pq",
    "multiplot",
    "multitax_bar_pq",
    "mumu_pq",
    "no_legend",
    "normalize_prop_pq",
    "otu_circle",
    "perc",
    "phyloseq_to_edgeR",
    "physeq_graph_test",
    "physeq_or_string_to_dna",
    "plot_ancombc_pq",
    "plot_complexity_pq",
    "plot_deseq2_phyloseq",
    "plot_deseq2_pq",
    "plot_edgeR_phyloseq",
    "plot_edgeR_pq",
    "plot_guild_pq",
    "plot_LCBD_pq",
    "plot_mt",
    "plot_refseq_extremity_pq",
    "plot_refseq_pq",
    "plot_SCBD_pq",
    "plot_seq_ratio_pq",
    "plot_tax_pq",
    "plot_tsne_pq",
    "plot_var_part_pq",
    "postcluster_pq",
    "psmelt_samples_pq",
    "rarefy_sample_count_by_modality",
    "read_phyloseq",
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    "rename_samples",
    "rename_samples_otu_table",
    "reorder_taxa_pq",
    "resolve_vector_ranks",
    "ridges_pq",
    "rotl_pq",
    "sam_data_matching_names",
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    "sankey_phyloseq",
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    "save_pq",
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    "signif_ancombc",
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    "subsample_fastq",
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    "subset_taxa_tax_control",
    "summary_plot_phyloseq",
    "summary_plot_pq",
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    "tbl_sum_samdata",
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    "treemap_pq",
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    "var_par_pq",
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    "vsearch_clustering",
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      "title": "Fungal OTU in phyloseq format",
      "object": "data_fungi",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "title": "Fungal OTU in phyloseq format",
      "object": "data_fungi_mini",
      "class": [
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      "table": false,
      "tojson": false
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      "name": "data_fungi_sp_known",
      "title": "Fungal OTU in phyloseq format",
      "object": "data_fungi_sp_known",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "Tengeler2020_pq",
      "title": "This tutorial explores the dataset from Tengeler et al. (2020) available in the 'mia' package. obtained using 'mia::makePhyloseqFromTreeSE(Tengeler2020)'",
      "object": "Tengeler2020_pq",
      "class": [
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    {
      "page": "MiscMetabar-package",
      "title": "'MiscMetabar' package",
      "topics": [
        "MiscMetabar-package"
      ]
    },
    {
      "page": "accu_plot",
      "title": "Plot accumulation curves for 'phyloseq-class' object",
      "topics": [
        "accu_plot"
      ]
    },
    {
      "page": "accu_plot_balanced_modality",
      "title": "Plot accumulation curves with balanced modality and depth rarefaction",
      "topics": [
        "accu_plot_balanced_modality"
      ]
    },
    {
      "page": "accu_samp_threshold",
      "title": "Compute the number of sequence to obtain a given proportion of ASV in accumulation curves",
      "topics": [
        "accu_samp_threshold"
      ]
    },
    {
      "page": "add_blast_info",
      "title": "Add information from 'blast_pq()' to the 'tax_table' slot of a _phyloseq_ object",
      "topics": [
        "add_blast_info"
      ]
    },
    {
      "page": "add_dna_to_phyloseq",
      "title": "Add dna in 'refseq' slot of a 'physeq' object using taxa names and renames taxa using prefix_taxa_names and number (default Taxa_1, Taxa_2 ...)",
      "topics": [
        "add_dna_to_phyloseq"
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    {
      "page": "add_funguild_info",
      "title": "Add information about Guild for FUNGI the FUNGuild databse",
      "topics": [
        "add_funguild_info"
      ]
    },
    {
      "page": "add_info_to_sam_data",
      "title": "Add information to sample_data slot of a phyloseq-class object",
      "topics": [
        "add_info_to_sam_data"
      ]
    },
    {
      "page": "add_new_taxonomy_pq",
      "title": "Add new taxonomic rank to a phyloseq object.",
      "topics": [
        "add_new_taxonomy_pq"
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    {
      "page": "adonis_pq",
      "title": "Permanova on a phyloseq object",
      "topics": [
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    },
    {
      "page": "adonis_rarperm_pq",
      "title": "Permanova (adonis) on permutations of rarefaction even depth",
      "topics": [
        "adonis_rarperm_pq"
      ]
    },
    {
      "page": "all_object_size",
      "title": "List the size of all objects of the GlobalEnv.",
      "topics": [
        "all_object_size"
      ]
    },
    {
      "page": "ancombc_pq",
      "title": "Run ANCOMBC2 on phyloseq object",
      "topics": [
        "ancombc_pq"
      ]
    },
    {
      "page": "are_modality_even_depth",
      "title": "Test if the mean number of sequences by samples is link to the modality of a factor",
      "topics": [
        "are_modality_even_depth"
      ]
    },
    {
      "page": "as_binary_otu_table",
      "title": "Transform the otu_table of a 'phyloseq-class' object into a 'phyloseq-class' object with a binary otu_table.",
      "topics": [
        "as_binary_otu_table"
      ]
    },
    {
      "page": "assign_blastn",
      "title": "Assign taxonomy using blastn algorithm and the blast software",
      "topics": [
        "assign_blastn"
      ]
    },
    {
      "page": "assign_dada2",
      "title": "Assign taxonomy with dada2 using 2 steps assignTaxonomy and assignSpecies",
      "topics": [
        "assign_dada2"
      ]
    },
    {
      "page": "assign_idtaxa",
      "title": "A wrapper of 'IdTaxa'",
      "topics": [
        "assign_idtaxa"
      ]
    },
    {
      "page": "assign_sintax",
      "title": "Assign Taxonomy using Sintax algorithm of Vsearch",
      "topics": [
        "assign_sintax"
      ]
    },
    {
      "page": "assign_vsearch_lca",
      "title": "Assign taxonomy using LCA",
      "topics": [
        "assign_vsearch_lca"
      ]
    },
    {
      "page": "biplot_pq",
      "title": "Visualization of two samples for comparison",
      "topics": [
        "biplot_pq"
      ]
    },
    {
      "page": "blast_pq",
      "title": "Blast all sequence of 'refseq' slot of a 'phyloseq-class' object against a custom database.",
      "topics": [
        "blast_pq"
      ]
    },
    {
      "page": "blast_to_derep",
      "title": "Blast some sequence against sequences from of a 'derep-class' object.",
      "topics": [
        "blast_to_derep"
      ]
    },
    {
      "page": "blast_to_phyloseq",
      "title": "Blast some sequence against 'refseq' slot of a 'phyloseq-class' object.",
      "topics": [
        "blast_to_phyloseq"
      ]
    },
    {
      "page": "build_phytree_pq",
      "title": "Build phylogenetic trees from refseq slot of a phyloseq object",
      "topics": [
        "build_phytree_pq"
      ]
    },
    {
      "page": "chimera_detection_vs",
      "title": "Detect for chimera taxa using vsearch",
      "topics": [
        "chimera_detection_vs"
      ]
    },
    {
      "page": "chimera_removal_vs",
      "title": "Search for a list of sequence in an object to remove chimera taxa using vsearch",
      "topics": [
        "chimera_removal_vs"
      ]
    },
    {
      "page": "circle_pq",
      "title": "Plot OTU circle for 'phyloseq-class' object",
      "topics": [
        "circle_pq"
      ]
    },
    {
      "page": "clean_pq",
      "title": "Clean phyloseq object by removing empty samples and taxa",
      "topics": [
        "clean_pq"
      ]
    },
    {
      "page": "compare_pairs_pq",
      "title": "Compare samples in pairs using diversity and number of ASV including shared ASV.",
      "topics": [
        "compare_pairs_pq"
      ]
    },
    {
      "page": "count_seq",
      "title": "Count sequences in fasta or fastq file",
      "topics": [
        "count_seq"
      ]
    },
    {
      "page": "cutadapt_remove_primers",
      "title": "Remove primers using cutadapt",
      "topics": [
        "cutadapt_remove_primers"
      ]
    },
    {
      "page": "data_fungi",
      "title": "Fungal OTU in phyloseq format",
      "topics": [
        "data_fungi"
      ]
    },
    {
      "page": "data_fungi_mini",
      "title": "Fungal OTU in phyloseq format",
      "topics": [
        "data_fungi_mini"
      ]
    },
    {
      "page": "data_fungi_sp_known",
      "title": "Fungal OTU in phyloseq format",
      "topics": [
        "data_fungi_sp_known"
      ]
    },
    {
      "page": "diff_fct_diff_class",
      "title": "Compute different functions for different class of vector.",
      "topics": [
        "diff_fct_diff_class"
      ]
    },
    {
      "page": "dist_bycol",
      "title": "Compute paired distances among matrix (e.g. otu_table)",
      "topics": [
        "dist_bycol"
      ]
    },
    {
      "page": "dist_pos_control",
      "title": "Calculate ecological distance among positive controls vs distance for all samples",
      "topics": [
        "dist_pos_control"
      ]
    },
    {
      "page": "distri_1_taxa",
      "title": "Distribution of sequences across a factor for one taxon",
      "topics": [
        "distri_1_taxa"
      ]
    },
    {
      "page": "fac2col",
      "title": "Translates a factor into colors.",
      "topics": [
        "fac2col"
      ]
    },
    {
      "page": "filt_taxa_pq",
      "title": "Filter taxa of a phyloseq object based on the minimum number of sequences/samples",
      "topics": [
        "filt_taxa_pq"
      ]
    },
    {
      "page": "filt_taxa_wo_NA",
      "title": "Filter taxa by cleaning taxa with NA at given taxonomic rank(s)",
      "topics": [
        "filt_taxa_wo_NA"
      ]
    },
    {
      "page": "filter_asv_blast",
      "title": "Filter undesirable taxa using blast against a custom database.",
      "topics": [
        "filter_asv_blast",
        "filter_taxa_blast"
      ]
    },
    {
      "page": "filter_trim",
      "title": "A wrapper of the function 'dada2::filterAndTrim()' to use in targets pipeline",
      "topics": [
        "filter_trim"
      ]
    },
    {
      "page": "format2dada2",
      "title": "Format a fasta database in dada2 format",
      "topics": [
        "format2dada2"
      ]
    },
    {
      "page": "format2dada2_species",
      "title": "Format a fasta database in dada2 format for Species assignment",
      "topics": [
        "format2dada2_species"
      ]
    },
    {
      "page": "format2sintax",
      "title": "Format a fasta database in sintax format",
      "topics": [
        "format2sintax"
      ]
    },
    {
      "page": "formattable_pq",
      "title": "Create a visualization table to describe taxa distribution across a modality",
      "topics": [
        "formattable_pq"
      ]
    },
    {
      "page": "funguild_assign",
      "title": "Assign Guilds to Organisms Based on Taxonomic Classification",
      "topics": [
        "funguild_assign"
      ]
    },
    {
      "page": "funky_color",
      "title": "Funky palette color",
      "topics": [
        "funky_color"
      ]
    },
    {
      "page": "get_file_extension",
      "title": "Get the extension of a file",
      "topics": [
        "get_file_extension"
      ]
    },
    {
      "page": "get_funguild_db",
      "title": "Retrieve the FUNGuild database",
      "topics": [
        "get_funguild_db"
      ]
    },
    {
      "page": "ggaluv_pq",
      "title": "Alluvial plot for taxonomy and samples factor vizualisation",
      "topics": [
        "ggaluv_pq"
      ]
    },
    {
      "page": "ggbetween_pq",
      "title": "Box/Violin plots for between-subjects comparisons of Hill Number",
      "topics": [
        "ggbetween_pq"
      ]
    },
    {
      "page": "ggscatt_pq",
      "title": "Scatterplot with marginal distributions and statistical results against Hill diversity of phyloseq object",
      "topics": [
        "ggscatt_pq"
      ]
    },
    {
      "page": "ggvenn_pq",
      "title": "Venn diagram of 'phyloseq-class' object using 'ggVennDiagram::ggVennDiagram' function",
      "topics": [
        "ggvenn_pq"
      ]
    },
    {
      "page": "glmutli_pq",
      "title": "Automated model selection and multimodel inference with (G)LMs for phyloseq",
      "topics": [
        "glmutli_pq"
      ]
    },
    {
      "page": "graph_test_pq",
      "title": "Performs graph-based permutation tests on phyloseq object",
      "topics": [
        "graph_test_pq"
      ]
    },
    {
      "page": "hill_curves_pq",
      "title": "Hill Diversities and Corresponding Accumulation Curves for phyloseq",
      "topics": [
        "hill_curves_pq"
      ]
    },
    {
      "page": "hill_pq",
      "title": "Graphical representation of hill number 0, 1 and 2 across a factor",
      "topics": [
        "hill_pq"
      ]
    },
    {
      "page": "hill_test_rarperm_pq",
      "title": "Test multiple times effect of factor on Hill diversity with different rarefaction even depth",
      "topics": [
        "hill_test_rarperm_pq"
      ]
    },
    {
      "page": "hill_tuckey_pq",
      "title": "Calculate hill number and compute Tuckey post-hoc test",
      "topics": [
        "hill_tuckey_pq"
      ]
    },
    {
      "page": "iNEXT_pq",
      "title": "iNterpolation and EXTrapolation of Hill numbers (with iNEXT)",
      "topics": [
        "iNEXT_pq"
      ]
    },
    {
      "page": "is_cutadapt_installed",
      "title": "Test if cutadapt is installed.",
      "topics": [
        "is_cutadapt_installed"
      ]
    },
    {
      "page": "is_falco_installed",
      "title": "Test if falco is installed.",
      "topics": [
        "is_falco_installed"
      ]
    },
    {
      "page": "is_krona_installed",
      "title": "Test if krona is installed.",
      "topics": [
        "is_krona_installed"
      ]
    },
    {
      "page": "is_mumu_installed",
      "title": "Test if mumu is installed.",
      "topics": [
        "is_mumu_installed"
      ]
    },
    {
      "page": "is_swarm_installed",
      "title": "Test if swarm is installed.",
      "topics": [
        "is_swarm_installed"
      ]
    },
    {
      "page": "is_vsearch_installed",
      "title": "Test if vsearch is installed.",
      "topics": [
        "is_vsearch_installed"
      ]
    },
    {
      "page": "krona",
      "title": "Make Krona files using KronaTools.",
      "topics": [
        "krona"
      ]
    },
    {
      "page": "LCBD_pq",
      "title": "Compute and test local contributions to beta diversity (LCBD) of samples",
      "topics": [
        "LCBD_pq"
      ]
    },
    {
      "page": "learn_idtaxa",
      "title": "A wrapper of 'DECIPHER::LearnTaxa()'",
      "topics": [
        "learn_idtaxa"
      ]
    },
    {
      "page": "list_fastq_files",
      "title": "List fastq files",
      "topics": [
        "list_fastq_files"
      ]
    },
    {
      "page": "lulu",
      "title": "Post Clustering Curation of Amplicon Data.",
      "topics": [
        "lulu"
      ]
    },
    {
      "page": "lulu_pq",
      "title": "Lulu reclustering of class 'physeq'",
      "topics": [
        "lulu_pq"
      ]
    },
    {
      "page": "merge_krona",
      "title": "Merge Krona files using KronaTools.",
      "topics": [
        "merge_krona"
      ]
    },
    {
      "page": "merge_samples2",
      "title": "Merge samples by a sample variable or factor",
      "topics": [
        "merge_samples2",
        "merge_samples2,otu_table-method",
        "merge_samples2,phyloseq-method",
        "merge_samples2,sample_data-method"
      ]
    },
    {
      "page": "merge_taxa_vec",
      "title": "Merge taxa in groups (vectorized version)",
      "topics": [
        "merge_taxa_vec",
        "merge_taxa_vec,otu_table-method",
        "merge_taxa_vec,phylo-method",
        "merge_taxa_vec,phyloseq-method",
        "merge_taxa_vec,taxonomyTable-method",
        "merge_taxa_vec,XStringSet-method"
      ]
    },
    {
      "page": "MiscMetabar-deprecated",
      "title": "Deprecated function(s) in the MiscMetabar package",
      "topics": [
        "adonis_phyloseq",
        "biplot_physeq",
        "clean_physeq",
        "ggVenn_phyloseq",
        "hill_phyloseq",
        "hill_tuckey_phyloseq",
        "lulu_phyloseq",
        "MiscMetabar-deprecated",
        "otu_circle",
        "physeq_graph_test",
        "plot_deseq2_phyloseq",
        "plot_edgeR_phyloseq",
        "read_phyloseq",
        "sankey_phyloseq",
        "summary_plot_phyloseq",
        "venn_phyloseq",
        "write_phyloseq"
      ]
    },
    {
      "page": "multi_biplot_pq",
      "title": "Visualization of a collection of couples of samples for comparison",
      "topics": [
        "multi_biplot_pq"
      ]
    },
    {
      "page": "multipatt_pq",
      "title": "Test and plot multipatt result",
      "topics": [
        "multipatt_pq"
      ]
    },
    {
      "page": "multiplot",
      "title": "Multiple plot function",
      "topics": [
        "multiplot"
      ]
    },
    {
      "page": "multitax_bar_pq",
      "title": "Plot taxonomic distribution across 3 taxonomic levels and optionally one sample factor",
      "topics": [
        "multitax_bar_pq"
      ]
    },
    {
      "page": "mumu_pq",
      "title": "MUMU reclustering of class 'physeq'",
      "topics": [
        "mumu_pq"
      ]
    },
    {
      "page": "no_legend",
      "title": "Discard legend in ggplot2",
      "topics": [
        "no_legend"
      ]
    },
    {
      "page": "normalize_prop_pq",
      "title": "Normalize OTU table using samples depth",
      "topics": [
        "normalize_prop_pq"
      ]
    },
    {
      "page": "perc",
      "title": "Convert a value (or a fraction x/y) in percentage",
      "topics": [
        "perc"
      ]
    },
    {
      "page": "phyloseq_to_edgeR",
      "title": "Convert phyloseq OTU count data into DGEList for edgeR package",
      "topics": [
        "phyloseq_to_edgeR"
      ]
    },
    {
      "page": "physeq_or_string_to_dna",
      "title": "Return a DNAStringSet object from either a character vector of DNA sequences or the 'refseq' slot of a phyloseq-class object",
      "topics": [
        "physeq_or_string_to_dna"
      ]
    },
    {
      "page": "plot_ancombc_pq",
      "title": "Plot ANCOMBC2 result for phyloseq object",
      "topics": [
        "plot_ancombc_pq"
      ]
    },
    {
      "page": "plot_complexity_pq",
      "title": "Plot kmer complexity of references sequences of a phyloseq object",
      "topics": [
        "plot_complexity_pq"
      ]
    },
    {
      "page": "plot_deseq2_pq",
      "title": "Plot DESeq2 results for a phyloseq or a DESeq2 object.",
      "topics": [
        "plot_deseq2_pq"
      ]
    },
    {
      "page": "plot_edgeR_pq",
      "title": "Plot edgeR results for a phyloseq or a edgeR object.",
      "topics": [
        "plot_edgeR_pq"
      ]
    },
    {
      "page": "plot_guild_pq",
      "title": "Plot information about Guild from tax_table slot previously created with 'add_funguild_info()'",
      "topics": [
        "plot_guild_pq"
      ]
    },
    {
      "page": "plot_LCBD_pq",
      "title": "Plot and test local contributions to beta diversity (LCBD) of samples",
      "topics": [
        "plot_LCBD_pq"
      ]
    },
    {
      "page": "plot_mt",
      "title": "Plot the result of a mt test 'phyloseq::mt()'",
      "topics": [
        "plot_mt"
      ]
    },
    {
      "page": "plot_refseq_extremity_pq",
      "title": "Plot the nucleotide proportion at both extremity of the sequences",
      "topics": [
        "plot_refseq_extremity_pq"
      ]
    },
    {
      "page": "plot_refseq_pq",
      "title": "Plot the nucleotide proportion of references sequences",
      "topics": [
        "plot_refseq_pq"
      ]
    },
    {
      "page": "plot_SCBD_pq",
      "title": "Plot species contributions to beta diversity (SCBD) of samples",
      "topics": [
        "plot_SCBD_pq"
      ]
    },
    {
      "page": "plot_seq_ratio_pq",
      "title": "A diagnostic plot of the number of sequences per samples",
      "topics": [
        "plot_seq_ratio_pq"
      ]
    },
    {
      "page": "plot_tax_pq",
      "title": "Plot taxonomic distribution in function of a factor with stacked bar in %",
      "topics": [
        "plot_tax_pq"
      ]
    },
    {
      "page": "plot_tsne_pq",
      "title": "Plot a tsne low dimensional representation of a phyloseq object",
      "topics": [
        "plot_tsne_pq"
      ]
    },
    {
      "page": "plot_var_part_pq",
      "title": "Plot the partition the variation of a phyloseq object",
      "topics": [
        "plot_var_part_pq"
      ]
    },
    {
      "page": "postcluster_pq",
      "title": "Recluster sequences of an object of class 'physeq' or a list of DNA sequences",
      "topics": [
        "asv2otu",
        "postcluster_pq"
      ]
    },
    {
      "page": "psmelt_samples_pq",
      "title": "Build a sample information tibble from physeq object",
      "topics": [
        "psmelt_samples_pq"
      ]
    },
    {
      "page": "rarefy_sample_count_by_modality",
      "title": "Rarefy (equalize) the number of samples per modality of a factor",
      "topics": [
        "rarefy_sample_count_by_modality"
      ]
    },
    {
      "page": "read_pq",
      "title": "Read phyloseq object from multiple csv tables and a phylogenetic tree in Newick format.",
      "topics": [
        "read_pq"
      ]
    },
    {
      "page": "rename_samples",
      "title": "Rename the samples of a phyloseq slot",
      "topics": [
        "rename_samples"
      ]
    },
    {
      "page": "rename_samples_otu_table",
      "title": "Rename samples of an otu_table",
      "topics": [
        "rename_samples_otu_table"
      ]
    },
    {
      "page": "reorder_taxa_pq",
      "title": "Reorder taxa in otu_table/tax_table/refseq slot of a phyloseq object",
      "topics": [
        "reorder_taxa_pq"
      ]
    },
    {
      "page": "resolve_vector_ranks",
      "title": "Resolve conflict in a vector of taxonomy values",
      "topics": [
        "resolve_vector_ranks"
      ]
    },
    {
      "page": "ridges_pq",
      "title": "Ridge plot of a phyloseq object",
      "topics": [
        "ridges_pq"
      ]
    },
    {
      "page": "rotl_pq",
      "title": "rotl wrapper for phyloseq data",
      "topics": [
        "rotl_pq"
      ]
    },
    {
      "page": "sam_data_matching_names",
      "title": "Match sample names from sam_data and fastq files",
      "topics": [
        "sam_data_matching_names"
      ]
    },
    {
      "page": "sample_data_with_new_names",
      "title": "Load sample data from file and rename samples using names of samples and an optional order",
      "topics": [
        "sample_data_with_new_names"
      ]
    },
    {
      "page": "sankey_pq",
      "title": "Sankey plot of 'phyloseq-class' object",
      "topics": [
        "sankey_pq"
      ]
    },
    {
      "page": "save_pq",
      "title": "A wrapper of write_pq to save in all three possible formats",
      "topics": [
        "save_pq"
      ]
    },
    {
      "page": "search_exact_seq_pq",
      "title": "Search for exact matching of sequences",
      "topics": [
        "search_exact_seq_pq"
      ]
    },
    {
      "page": "select_one_sample",
      "title": "Select one sample from a physeq object",
      "topics": [
        "select_one_sample"
      ]
    },
    {
      "page": "select_taxa-methods",
      "title": "Select a subset of taxa in a specified order where possible",
      "topics": [
        "select_taxa",
        "select_taxa,otu_table,character-method",
        "select_taxa,phylo,character-method",
        "select_taxa,phyloseq,character-method",
        "select_taxa,sample_data,character-method",
        "select_taxa,taxonomyTable,character-method",
        "select_taxa,XStringSet,character-method"
      ]
    },
    {
      "page": "signif_ancombc",
      "title": "Filter ancombc_pq results",
      "topics": [
        "signif_ancombc"
      ]
    },
    {
      "page": "simplify_taxo",
      "title": "Simplify taxonomy by removing some unused characters such as \"k__\"",
      "topics": [
        "simplify_taxo"
      ]
    },
    {
      "page": "SRS_curve_pq",
      "title": "Scaling with ranked subsampling (SRS) curve of phyloseq object",
      "topics": [
        "SRS_curve_pq"
      ]
    },
    {
      "page": "subsample_fastq",
      "title": "Subsample a fastq file copying the n_seq first sequences in a given folder",
      "topics": [
        "subsample_fastq"
      ]
    },
    {
      "page": "subset_samples_pq",
      "title": "Subset samples using a conditional boolean vector.",
      "topics": [
        "subset_samples_pq"
      ]
    },
    {
      "page": "subset_taxa_pq",
      "title": "Subset taxa using a conditional named boolean vector.",
      "topics": [
        "subset_taxa_pq"
      ]
    },
    {
      "page": "subset_taxa_tax_control",
      "title": "Subset taxa using a taxa control or distribution based method",
      "topics": [
        "subset_taxa_tax_control"
      ]
    },
    {
      "page": "summary_plot_pq",
      "title": "Summarize a 'phyloseq-class' object using a plot.",
      "topics": [
        "summary_plot_pq"
      ]
    },
    {
      "page": "swarm_clustering",
      "title": "Re-cluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using SWARM",
      "topics": [
        "swarm_clustering"
      ]
    },
    {
      "page": "tax_bar_pq",
      "title": "Plot the distribution of sequences or ASV in one taxonomic levels",
      "topics": [
        "tax_bar_pq"
      ]
    },
    {
      "page": "tax_datatable",
      "title": "Make a datatable with the taxonomy of a 'phyloseq-class' object",
      "topics": [
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      "page": "taxa_as_columns",
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      "topics": [
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      "page": "taxa_only_in_one_level",
      "title": "Show taxa which are present in only one given level of a modality",
      "topics": [
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    },
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      "page": "tbl_sum_samdata",
      "title": "Summarize information from sample data in a table",
      "topics": [
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    },
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      "page": "tbl_sum_taxtable",
      "title": "Summarize a tax_table (taxonomic slot of phyloseq object) using gtsummary",
      "topics": [
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      "page": "Tengeler2020_pq",
      "title": "This tutorial explores the dataset from Tengeler et al. (2020) available in the 'mia' package. obtained using 'mia::makePhyloseqFromTreeSE(Tengeler2020)'",
      "topics": [
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    {
      "page": "track_wkflow",
      "title": "Track the number of reads (= sequences), samples and cluster (e.g. ASV) from various objects including dada-class and derep-class.",
      "topics": [
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    },
    {
      "page": "track_wkflow_samples",
      "title": "Track the number of reads (= sequences), samples and cluster (e.g. ASV) for each sample",
      "topics": [
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    {
      "page": "transp",
      "title": "Adds transparency to a vector of colors",
      "topics": [
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    {
      "page": "treemap_pq",
      "title": "Plot treemap of 2 taxonomic levels",
      "topics": [
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    {
      "page": "tsne_pq",
      "title": "Compute tSNE position of samples from a phyloseq object",
      "topics": [
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      "page": "umap_pq",
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      "topics": [
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      "page": "unique_or_na",
      "title": "Get the unique value in x or NA if none",
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      "page": "upset_pq",
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      "topics": [
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      "page": "upset_test_pq",
      "title": "Test for differences between intersections",
      "topics": [
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    {
      "page": "var_par_pq",
      "title": "Partition the Variation of a phyloseq object by 2, 3, or 4 Explanatory Matrices",
      "topics": [
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      "page": "var_par_rarperm_pq",
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      "page": "venn_pq",
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      "topics": [
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    {
      "page": "verify_pq",
      "title": "Verify the validity of a phyloseq object",
      "topics": [
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    {
      "page": "vs_search_global",
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      "topics": [
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    },
    {
      "page": "vsearch_clustering",
      "title": "Recluster sequences of an object of class 'physeq' or cluster a list of DNA sequences using vsearch software",
      "topics": [
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    },
    {
      "page": "write_pq",
      "title": "Save phyloseq object in the form of multiple csv tables.",
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      "source": "MiscMetabar.Rmd",
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      "title": "Introduction",
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      "headings": [
        "Introduction to MiscMetabar: an R package to facilitate visualization and reproducibility in metabarcoding analysis",
        "Raison d'être",
        "Quick overview",
        "Summarize a physeq object",
        "Create an interactive table of the tax_table",
        "Sankey diagram of the tax_table",
        "Upset plot for visualize distribution of taxa in function of samples variables",
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        "Session inform"
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      "created": "2026-05-19 02:02:00",
      "modified": "2026-05-19 02:02:00",
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