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 explore the dataset from Tengeler
                        et al. (2020) available in the 'mia' package.
                        obtain using
                        'mia::makePhyloseqFromTreeSE(Tengeler2020)'
accu_plot               Plot accumulation curves for 'phyloseq-class'
                        object
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 ASV_1,
                        ASV_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
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.
asv2otu                 Recluster sequences of an object of class
                        'physeq' or a list of DNA sequences
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
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
filter_asv_blast        Filter undesirable taxa using blast against a
                        against a custom database.
filter_trim             A wrapper of the function
                        'dada2::filterAndTrim()' to use in targets
                        pipeline
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
ggbetween_pq            Box/Violin plots for between-subjects
                        comparisons of Hill Number
ggvenn_pq               Venn diagram of 'phyloseq-class' object using
                        'ggVennDiagram::ggVennDiagram' function
graph_test_pq           Performs graph-based permutation tests on
                        phyloseq object
heat_tree_pq            Heat tree from 'metacoder' package using
                        'tax_table' slot
hill_pq                 Graphical representation of hill number 0, 1
                        and 2 across a factor
hill_tuckey_pq          Calculate hill number and compute Tuckey
                        post-hoc test
iNEXT_pq                iNterpolation and EXTrapolation of Hill numbers
                        (with iNEXT)
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_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.
list_fastq_files        List fastq files
lulu                    Post Clustering Curation of Amplicon Data.
lulu_pq                 Lulu reclustering of class 'physeq'
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)
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'
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_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_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
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_taxa_pq         Reorder taxa in otu_table/tax_table/refseq slot
                        of a phyloseq object
ridges_pq               Ridge plot of a phyloseq object
rotl_pq                 rotl wrapper for phyloseq data
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 using
                        complement, reverse and reverse-complement
select_one_sample       Select one sample from a physeq object
select_taxa             Select a subset of taxa in a specified order
                        where possible
simplify_taxo           Simplify taxonomy by removing some unused
                        characters such as "k__"
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 (e.g. truffle
                        root tips) through 3 methods.
summary_plot_pq         Summarise 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
tbl_sum_samdata         Summarize information from sample data in a
                        table
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
                        samples.
treemap_pq              Plot treemap of 2 taxonomic levels
tsne_pq                 Compute tSNE position of samples from a
                        phyloseq object
unique_or_na            Get the unique value in x or NA if none
upset_pq                Make upset plot for phyloseq object.
upset_test_pq           Test for differences between intersections
venn_pq                 Venn diagram of 'phyloseq-class' object
verify_pq               Verify the validity 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
write_pq                Save phyloseq object in the form of multiple
                        csv tables.
