aaDistribution          Amino acid distribution of sequences
aaseqtab                Summary of amino acid sequences of B cells of
                        one individual
aaseqtab2               Summary of amino acid sequences of B cells of
                        another individual
bcRep-package           Advanced Analysis of B Cell Receptor Repertoire
                        Data
clones                  Grouping sequences into clones
clones.CDR3Length       CDR3 length distribution of clones
clones.allind           B cell clones of 8 individuals
clones.filterFunctionality
                        Filter for productive/unproductive clones
clones.filterJunctionFrame
                        Filter for in-frame/out-of-frame clones
clones.filterSize       Filter clones for their size
clones.giniIndex        Gini index of clones
clones.ind              Data frame: clones of one individual
clones.shared           Shared clones between samples
combineIMGT             Combination of several IMGT output folders
compare.aaDistribution
                        Compare amino acid distribution of different
                        samples
compare.geneUsage       Compare gene usage of different samples
compare.trueDiversity   Compare richness or diversity of different
                        samples
dist.PCoA               Principal coordinate analysis (PCoA;
                        multidimensional scaling [MDS]) of
                        dissimilarity/distance indices
geneUsage               Gene usage statistics
geneUsage.distance      Dissimilarity/distance indices for gene usage
                        data
mutationtab             Summary of mutations cells
ntseqtab                Summary of nucleotide sequences of B cells of
                        one individual
plotClonesCopyNumber    Copy number of clones
readIMGT                Read IMGT/HighV-QUEST output files
sequences.distance      Dissimilarity/distance indices for sequence
                        data
sequences.functionality
                        Summary of functionality of sequences
sequences.geneComb      Gene/gene combinations
sequences.getAnyFunctionality
                        Filter for productive or unproductive sequences
sequences.getAnyJunctionFrame
                        Filter for in-frame or out-of-frame sequences
sequences.junctionFrame
                        Summary of junction frames of sequences
sequences.mutation      Basic statistics on mutations of sequences
sequences.mutation.AA   Detect amino acid mutations in V-, FR- or
                        CDR-regions
sequences.mutation.base
                        Statistics about silent mutations
summarytab              Summary information of B cells of one
                        individual
trueDiversity           True diversity of sequences
vgenes                  VH gene usage data
