.quant_column_choice    Get a column's name using the input alias
aa_properties           Tables with amino acid properties
aa_table                Amino acid / codon table
add_class               Add a new class attribute
airr_clonality          Clonality - receptor overabundance statistics
                        for immune repertoires
airr_diversity          Diversity - estimating the heterogeneity of
                        immune repertoires
airr_public             Public indices - pairwise repertoire overlap
airr_stats              Compute key immune repertoire statistics
annotate_clonality      Annotate clonality - per-receptor labels for
                        overabundance
apply_symm              Apply function to each pair of data frames from
                        a list.
bcrdata                 BCR dataset
bunch_translate         Nucleotide to amino acid sequence translation
check_distribution      Check and normalise distributions
coding                  Filter out coding and non-coding clonotype
                        sequences
dbAnnotate              Annotate clonotypes in immune repertoires using
                        clonotype databases (e.g., VDJDB, McPAS)
dbLoad                  Load clonotype databases such as VDJDB and
                        McPAS into the R workspace
entropy                 Information measures
fixVis                  Manipulate ggplot plots and create
                        publication-ready plots
geneUsage               Main function for estimation of V-gene and
                        J-gene statistics
geneUsageAnalysis       Post-analysis of V-gene and J-gene statistics:
                        PCA, clustering, etc.
gene_segments           Gene segments table
gene_stats              WIP
getKmers                Calculate the k-mer statistics of immune
                        repertoires
get_immunarch_news      Get the Latest immunarch Update
group_from_metadata     Get a character vector of samples' groups from
                        the input metadata file
has_class               Check for the specific class
immdata                 Single chain immune repertoire dataset
immunarch_v1_updates    Get a list of package updates
immunr_data_format      Specification of the data format used by
                        immunarch dataframes
immunr_hclust           Clustering of objects or distance matrices
immunr_pca              Dimensionality reduction
inc_overlap             Incremental counting of repertoire similarity
list_immunarch_news     List Available immunarch Updates
matrixdiagcopy          Copy the upper matrix triangle to the lower one
pubRep                  Create a repertoire of public clonotypes
pubRepApply             Apply transformations to public repertoires
pubRepFilter            Filter out clonotypes from public repertoires
pubRepStatistics        Statistics of number of public clonotypes for
                        each possible combinations of repertoires
public_matrix           Get a matrix with public clonotype frequencies
repAlignLineage         Aligns all sequences incliding germline within
                        each clonal lineage within each cluster
repClonalFamily         Builds a phylogenetic tree using the sequences
                        of a clonal lineage
repClonality            Clonality analysis of immune repertoires
repDiversity            The main function for immune repertoire
                        diversity estimation
repExplore              Main function for exploratory data analysis:
                        compute the distribution of lengths, clones,
                        etc.
repFilter               Main function for data filtering
repGermline             Creates germlines for clonal lineages
repLoad                 Load immune repertoire files into the R
                        workspace
repOverlap              Main function for public clonotype statistics
                        calculations
repOverlapAnalysis      Post-analysis of public clonotype statistics:
                        PCA, clustering, etc.
repSample               Downsampling and resampling of immune
                        repertoires
repSave                 Save immune repertoires to the disk
repSomaticHypermutation
                        Calculates number of mutations against the
                        germline for each clonotype
select_barcodes         Select specific clonotypes using barcodes from
                        single-cell metadata
select_clusters         Split the immune repertoire data to clusters
                        from single-cell barcodes
seqCluster              Function for assigning clusters based on
                        sequences similarity
seqDist                 Function for computing distance for sequences
set_pb                  Set and update progress bars
spectratype             Immune repertoire spectratyping
split_to_kmers          Analysis immune repertoire kmer statistics:
                        sequence profiles, etc.
switch_type             Return a column's name
top                     Get the N most abundant clonotypes
trackClonotypes         Track clonotypes across time and data points
vis                     One function to visualise them all
vis.clonal_family       Visualise clonal family tree: wrapper for
                        calling on the entire repClonalFamily output
vis.clonal_family_tree
                        Visualise clonal family tree
vis.immunr_chao1        Visualise diversity.
vis.immunr_clonal_prop
                        Visualise results of the clonality analysis
vis.immunr_dynamics     Visualise clonotype dynamics
vis.immunr_exp_vol      Visualise results of the exploratory analysis
vis.immunr_gene_usage   Histograms and boxplots (general case / gene
                        usage)
vis.immunr_hclust       Visualisation of hierarchical clustering
vis.immunr_inc_overlap
                        Visualise incremental overlaps
vis.immunr_kmeans       Visualisation of K-means and DBSCAN clustering
vis.immunr_kmer_table   Most frequent kmers visualisation.
vis.immunr_mds          PCA / MDS / tSNE visualisation (mainly overlap
                        / gene usage)
vis.immunr_ov_matrix    Repertoire overlap and gene usage
                        visualisations
vis.immunr_public_repertoire
                        Public repertoire visualisation
vis.immunr_public_statistics
                        Visualise sharing of clonotypes among samples
vis.step_failure_ignored
                        Handler for .nofail argument of pipeline steps
                        that prevents examples from crashing on
                        computers where certain dependencies are not
                        installed
vis_bar                 Bar plots
vis_box                 Flexible box-plots for visualisation of
                        distributions
vis_circos              Visualisation of matrices using circos plots
vis_heatmap             Visualisation of matrices and data frames using
                        ggplo2-based heatmaps
vis_heatmap2            Visualisation of matrices using pheatmap-based
                        heatmaps
vis_hist                Visualisation of distributions using histograms
vis_immunr_kmer_profile_main
                        Visualise kmer profiles
vis_public_clonotypes   Visualisation of public clonotypes
vis_public_frequencies
                        Public repertoire visualisation
vis_textlogo            Sequence logo plots for amino acid profiles.
