LCBD_pq                 Compute and test local contributions to beta
                        diversity (LCBD) of samples
MiscMetabar-deprecated
                        Deprecated function(s) in the MiscMetabar
                        package
MiscMetabar-package     'MiscMetabar' package
SRS_curve_pq            Scaling with ranked subsampling (SRS) curve of
                        phyloseq object
Tengeler2020_pq         This tutorial explores the dataset from
                        Tengeler et al. (2020) available in the 'mia'
                        package. obtained using
                        'mia::makePhyloseqFromTreeSE(Tengeler2020)'
accu_plot               Plot accumulation curves for 'phyloseq-class'
                        object
accu_plot_balanced_modality
                        Plot accumulation curves with balanced modality
                        and depth rarefaction
accu_samp_threshold     Compute the number of sequence to obtain a
                        given proportion of ASV in accumulation curves
add_blast_info          Add information from 'blast_pq()' to the
                        'tax_table' slot of a _phyloseq_ object
add_dna_to_phyloseq     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 ...)
add_funguild_info       Add information about Guild for FUNGI the
                        FUNGuild databse
add_info_to_sam_data    Add information to sample_data slot of a
                        phyloseq-class object
add_new_taxonomy_pq     Add new taxonomic rank to a phyloseq object.
adonis_pq               Permanova on a phyloseq object
adonis_rarperm_pq       Permanova (adonis) on permutations of
                        rarefaction even depth
aldex_pq                Run Aldex on a phyloseq object
all_object_size         List the size of all objects of the GlobalEnv.
ancombc_pq              Run ANCOMBC2 on phyloseq object
are_modality_even_depth
                        Test if the mean number of sequences by samples
                        is link to the modality of a factor
as_binary_otu_table     Transform the otu_table of a 'phyloseq-class'
                        object into a 'phyloseq-class' object with a
                        binary otu_table.
assign_blastn           Assign taxonomy using blastn algorithm and the
                        blast software
assign_dada2            Assign taxonomy with dada2 using 2 steps
                        assignTaxonomy and assignSpecies
assign_idtaxa           A wrapper of 'IdTaxa'
assign_mmseqs2          Assign taxonomy using MMseqs2
assign_sintax           Assign Taxonomy using Sintax algorithm of
                        Vsearch
assign_vsearch_lca      Assign taxonomy using LCA
biplot_pq               Visualization of two samples for comparison
blast_pq                Blast all sequence of 'refseq' slot of a
                        'phyloseq-class' object against a custom
                        database.
blast_to_derep          Blast some sequence against sequences from of a
                        'derep-class' object.
blast_to_phyloseq       Blast some sequence against 'refseq' slot of a
                        'phyloseq-class' object.
build_phytree_pq        Build phylogenetic trees from refseq slot of a
                        phyloseq object
chimera_detection_vs    Detect for chimera taxa using vsearch
chimera_removal_vs      Search for a list of sequence in an object to
                        remove chimera taxa using vsearch
circle_pq               Plot OTU circle for 'phyloseq-class' object
clean_pq                Clean phyloseq object by removing empty samples
                        and taxa
compare_pairs_pq        Compare samples in pairs using diversity and
                        number of ASV including shared ASV.
count_seq               Count sequences in fasta or fastq file
css_pq                  Cumulative Sum Scaling (CSS) normalization of a
                        phyloseq object
cutadapt_remove_primers
                        Remove primers using cutadapt
data_fungi              Fungal OTU in phyloseq format
data_fungi_mini         Fungal OTU in phyloseq format
data_fungi_sp_known     Fungal OTU in phyloseq format
diff_fct_diff_class     Compute different functions for different class
                        of vector.
dist_bycol              Compute paired distances among matrix (e.g.
                        otu_table)
dist_pos_control        Calculate ecological distance among positive
                        controls vs distance for all samples
distri_1_taxa           Distribution of sequences across a factor for
                        one taxon
divent_hill_matrix_pq   Compute Hill diversity numbers for all samples
                        in an OTU table
fac2col                 Translates a factor into colors.
filt_taxa_pq            Filter taxa of a phyloseq object based on the
                        minimum number of sequences/samples
filt_taxa_wo_NA         Filter taxa by cleaning taxa with NA at given
                        taxonomic rank(s)
filter_asv_blast        Filter undesirable taxa using blast against a
                        custom database.
filter_trim             A wrapper of the function
                        'dada2::filterAndTrim()' to use in targets
                        pipeline
find_mmseqs2            Find the MMseqs2 binary
find_vsearch            Find the vsearch binary
format2dada2            Format a fasta database in dada2 format
format2dada2_species    Format a fasta database in dada2 format for
                        Species assignment
format2sintax           Format a fasta database in sintax format
formattable_pq          Create a visualization table to describe taxa
                        distribution across a modality
funguild_assign         Assign Guilds to Organisms Based on Taxonomic
                        Classification
funky_color             Funky palette color
get_file_extension      Get the extension of a file
get_funguild_db         Retrieve the FUNGuild database
ggaluv_pq               Alluvial plot for taxonomy and samples factor
                        vizualisation
ggbetween_pq            Box/Violin plots for between-subjects
                        comparisons of Hill Number
ggscatt_pq              Scatterplot with marginal distributions and
                        statistical results against Hill diversity of
                        phyloseq object
ggvenn_pq               Venn diagram of 'phyloseq-class' object using
                        'ggVennDiagram::ggVennDiagram' function
glmutli_pq              Automated model selection and multimodel
                        inference with (G)LMs for phyloseq
gmpr_pq                 Geometric Mean of Pairwise Ratios (GMPR)
                        normalization of a phyloseq object
graph_test_pq           Performs graph-based permutation tests on
                        phyloseq object
hill_acc_pq             Hill diversity accumulation curve for a
                        phyloseq object (default: q = 1)
hill_bar_pq             Bar plot of Hill diversity with SE, jittered
                        points, and Kruskal-Wallis test
hill_curves_pq          Hill Diversities and Corresponding Accumulation
                        Curves for phyloseq
hill_pq                 Graphical representation of hill number 0, 1
                        and 2 across a factor
hill_test_rarperm_pq    Test multiple times effect of factor on Hill
                        diversity with different rarefaction even depth
hill_tuckey_pq          Calculate hill number and compute Tuckey
                        post-hoc test
iNEXT_pq                iNterpolation and EXTrapolation of Hill numbers
                        (with iNEXT)
install_mmseqs2         Install MMseqs2 from GitHub releases
install_vsearch         Install vsearch binary
is_cutadapt_installed   Test if cutadapt is installed.
is_falco_installed      Test if falco is installed.
is_krona_installed      Test if krona is installed.
is_mmseqs2_installed    Check whether MMseqs2 is installed and callable
is_mumu_installed       Test if mumu is installed.
is_swarm_installed      Test if swarm is installed.
is_vsearch_installed    Test if vsearch is installed.
krona                   Make Krona files using KronaTools.
learn_idtaxa            A wrapper of 'DECIPHER::LearnTaxa()'
lefser_pq               Run LEfSe on a phyloseq object
list_fastq_files        List fastq files
lulu                    Post Clustering Curation of Amplicon Data.
lulu_pq                 Lulu reclustering of class 'physeq'
mcknight_residuals_pq   Depth-robust alpha diversity residuals
                        (McKnight / Mikryukov)
merge_krona             Merge Krona files using KronaTools.
merge_samples2          Merge samples by a sample variable or factor
merge_taxa_vec          Merge taxa in groups (vectorized version)
mmseqs2_clustering      Recluster sequences of a phyloseq object or
                        cluster a list of DNA sequences using MMseqs2
                        software
multi_biplot_pq         Visualization of a collection of couples of
                        samples for comparison
multipatt_pq            Test and plot multipatt result
multiplot               Multiple plot function
multitax_bar_pq         Plot taxonomic distribution across 3 taxonomic
                        levels and optionally one sample factor
mumu_pq                 MUMU reclustering of class 'physeq'
no_legend               Discard legend in ggplot2
normalize_prop_pq       Normalize OTU table using samples depth
perc                    Convert a value (or a fraction x/y) in
                        percentage
phyloseq_to_edgeR       Convert phyloseq OTU count data into DGEList
                        for edgeR package
physeq_or_string_to_dna
                        Return a DNAStringSet object from either a
                        character vector of DNA sequences or the
                        'refseq' slot of a phyloseq-class object
plot_LCBD_pq            Plot and test local contributions to beta
                        diversity (LCBD) of samples
plot_SCBD_pq            Plot species contributions to beta diversity
                        (SCBD) of samples
plot_ancombc_pq         Plot ANCOMBC2 result for phyloseq object
plot_complexity_pq      Plot kmer complexity of references sequences of
                        a phyloseq object
plot_deseq2_pq          Plot DESeq2 results for a phyloseq or a DESeq2
                        object.
plot_edgeR_pq           Plot edgeR results for a phyloseq or a edgeR
                        object.
plot_guild_pq           Plot information about Guild from tax_table
                        slot previously created with
                        'add_funguild_info()'
plot_mt                 Plot the result of a mt test 'phyloseq::mt()'
plot_ordination_pq      A wrapper of plot_ordination with vegan
                        distance matrix
plot_refseq_extremity_pq
                        Plot the nucleotide proportion at both
                        extremity of the sequences
plot_refseq_pq          Plot the nucleotide proportion of references
                        sequences
plot_seq_ratio_pq       A diagnostic plot of the number of sequences
                        per samples
plot_tax_pq             Plot taxonomic distribution in function of a
                        factor with stacked bar in %
plot_tsne_pq            Plot a tsne low dimensional representation of a
                        phyloseq object
plot_var_part_pq        Plot the partition the variation of a phyloseq
                        object
postcluster_pq          Recluster sequences of an object of class
                        'physeq' or a list of DNA sequences
profile_hill_pq         Hill diversity profile for a phyloseq object
psmelt_samples_pq       Build a sample information tibble from physeq
                        object
rarefy_even_depth_pq    Rarefy a phyloseq object to even sequencing
                        depth
rarefy_pq               Rarefy a phyloseq object, optionally averaging
                        over repetitions
rarefy_sample_count_by_modality
                        Rarefy (equalize) the number of samples per
                        modality of a factor
read_pq                 Read phyloseq object from multiple csv tables
                        and a phylogenetic tree in Newick format.
rename_samples          Rename the samples of a phyloseq slot
rename_samples_otu_table
                        Rename samples of an otu_table
reorder_distinct_colors
                        Reorder fill and color scales to maximize
                        perceptual contrast between adjacent segments
reorder_taxa_pq         Reorder taxa in otu_table/tax_table/refseq slot
                        of a phyloseq object
resolve_vector_ranks    Resolve conflict in a vector of taxonomy values
ridges_pq               Ridge plot of a phyloseq object
ridges_sam_pq           Ridges plot of sample distribution across taxa
rotl_pq                 rotl wrapper for phyloseq data
sam_data_matching_names
                        Match sample names from sam_data and fastq
                        files
sample_data_with_new_names
                        Load sample data from file and rename samples
                        using names of samples and an optional order
sankey_pq               Sankey plot of 'phyloseq-class' object
save_pq                 A wrapper of write_pq to save in all three
                        possible formats
search_exact_seq_pq     Search for exact matching of sequences
select_one_sample       Select one sample from a physeq object
select_taxa             Select a subset of taxa in a specified order
                        where possible
signif_ancombc          Filter ancombc_pq results
simplify_taxo           Simplify taxonomy by removing some unused
                        characters such as "k__"
srs_pq                  Scaling with Ranked Subsampling (SRS)
                        normalization of a phyloseq object
subsample_fastq         Subsample a fastq file copying the n_seq first
                        sequences in a given folder
subset_samples_pq       Subset samples using a conditional boolean
                        vector.
subset_taxa_pq          Subset taxa using a conditional named boolean
                        vector.
subset_taxa_tax_control
                        Subset taxa using a taxa control or
                        distribution based method
summary_plot_pq         Summarize a 'phyloseq-class' object using a
                        plot.
swarm_clustering        Re-cluster sequences of an object of class
                        'physeq' or cluster a list of DNA sequences
                        using SWARM
tax_bar_pq              Plot the distribution of sequences or ASV in
                        one taxonomic levels
tax_datatable           Make a datatable with the taxonomy of a
                        'phyloseq-class' object
taxa_as_columns         Force taxa to be in columns in the otu_table of
                        a physeq object
taxa_as_rows            Force taxa to be in columns in the otu_table of
                        a physeq object
taxa_only_in_one_level
                        Show taxa which are present in only one given
                        level of a modality
tbl_sum_samdata         Summarize information from sample data in a
                        table
tbl_sum_taxtable        Summarize a tax_table (taxonomic slot of
                        phyloseq object) using gtsummary
tmm_pq                  Trimmed Mean of M-values (TMM) normalization of
                        a phyloseq object
track_wkflow            Track the number of reads (= sequences),
                        samples and cluster (e.g. ASV) from various
                        objects including dada-class and derep-class.
track_wkflow_samples    Track the number of reads (= sequences),
                        samples and cluster (e.g. ASV) for each sample
transform_pq            Unified dispatcher for all OTU-table
                        transformations and normalisations
transp                  Adds transparency to a vector of colors
treemap_pq              Plot treemap of 2 taxonomic levels
tsne_pq                 Compute tSNE position of samples from a
                        phyloseq object
umap_pq                 Computes a manifold approximation and
                        projection (UMAP) for phyloseq object
unique_or_na            Get the unique value in x or NA if none
unwanted_tax_patterns   Default patterns for unwanted taxonomic values
upset_pq                Make upset plot for phyloseq object.
upset_test_pq           Test for differences between intersections
var_par_pq              Partition the Variation of a phyloseq object by
                        2, 3, or 4 Explanatory Matrices
var_par_rarperm_pq      Partition the Variation of a phyloseq object
                        with rarefaction permutations
venn_pq                 Venn diagram of 'phyloseq-class' object
verify_pq               Verify the validity of a phyloseq object
verify_tax_table        Verify the taxonomy table of a phyloseq object
vs_search_global        Search for a list of sequence in a fasta file
                        against physeq reference sequences using
                        vsearch
vsearch_clustering      Recluster sequences of an object of class
                        'physeq' or cluster a list of DNA sequences
                        using vsearch software
vst_pq                  Variance Stabilizing Transformation of a
                        phyloseq object (DESeq2)
write_pq                Save phyloseq object in the form of multiple
                        csv tables.
