.add.legend             Internal function. Add legend to a grid of
                        plots and remove legend from all plots of a
                        grid.
.column.choice          Choose the right column.
.fix.listnames          Fix names in lists.
.verbose.msg            Print the given message if second parameter is
                        a TRUE.
AA_TABLE                Tables with genetic code.
apply.symm              Apply function to every pair of data frames
                        from a list.
assymetry               Normalised log assymetry.
barcodes.to.reads       Rearrange columns with counts for clonesets.
beta.prob               List with assembling probabilities of beta
                        chain TCRs.
bootstrap.tcr           Bootstrap for data frames in package tcR.
check.distribution      Check for adequaty of distrubution.
clonal.space.homeostasis
                        Clonal space homeostasis.
cloneset.stats          MiTCR data frame basic statistics.
codon.variants          Functions for working with aminoacid sequences.
column.summary          Columns statistics.
contamination.stats     Contamination filtering.
convergence.index       Compute convergence characteristics of
                        repertoires.
cosine.sharing          Shared repertoire analysis.
cosine.similarity       Set and vector similarity measures.
entropy                 Information measures.
entropy.seg             Repertoires' analysis using information
                        measures applied to V- and J- segment
                        frequencies.
find.clonotypes         Find target clonotypes and get columns' value
                        corresponded to that clonotypes.
find.similar.sequences
                        Find similar sequences.
fix.alleles             Fix alleles / genes by removing allele
                        information / unnecessary colons.
gc.content              GC-content of a nucleotide sequences.
geneUsage               Gene usage.
generate.kmers          Generate k-mers.
generate.tcr            Generate random nucleotide TCR sequences.
get.all.substrings      Get all substrings for the given sequence.
get.deletions.alpha     Compute the number of deletions in MiTCR data
                        frames.
get.inframes            In-frame / out-of-frame sequences filter.
get.kmers               Get kmers from sequences.
gibbs.sampler           Gibbs Sampler.
group.clonotypes        Get all unique clonotypes.
has.class               Check if a given object has a given class.
intersectClonesets      Intersection between sets of sequences or any
                        elements.
inverse.simpson         Distribution evaluation.
kmer.profile            Profile of sequences of equal length.
kmer.table              Make and manage the table of the most frequent
                        k-mers.
loglikelihood           Log-likelihood.
matrixSubgroups         Get all values from the matrix corresponding to
                        specific groups.
matrixdiagcopy          Copy the up-triangle matrix values to
                        low-triangle.
mutated.neighbours      Get vertex neighbours.
mutation.network        Make mutation network for the given repertoire.
ozScore                 Overlap Z-score.
parse.cloneset          Parse input table files with the immune
                        receptor repertoire data.
parse.folder            Parse input table files with immune receptor
                        repertoire data.
pca.segments            Perform PCA on segments frequency data.
pca2euclid              Compute the Euclidean distance among principal
                        components.
permutDistTest          Monte Carlo permutation test for pairwise and
                        one-vs-all-wise within- and inter-group
                        differences in a set of repertoires.
permutedf               Shuffling data frames.
rarefaction             Diversity evaluation using rarefaction.
repDiversity            General function for the repertoire diversity
                        estimation.
repLoad                 Parse input files or folders with immune
                        receptor repertoire data.
repOverlap              General function for the repertoire overlap
                        evaluation.
repSave                 Save tcR data frames to disk as text files or
                        gzipped text files.
resample                Resample data frame using values from the
                        column with number of clonesets.
revcomp                 DNA reverse complementing and translation.
reverse.string          Reverse given character vector by the given
                        n-plets.
sample.clones           Get a random subset from a data.frame.
sample2D                Get a sample from matrix with probabilities.
segments.alphabets      Alphabets of TCR and Ig gene segments.
segments.list           Segment data.
set.group.vector        Set group attribute for vertices of a mutation
                        network
set.pb                  Simple functions for manipulating progress
                        bars.
set.people.vector       Set and get attributes of a mutation network
                        related to source people.
set.rank                Set new columns "Rank" and "Index".
shared.repertoire       Shared TCR repertoire managing and analysis
spectratype             Spectratype
startmitcr              Start MiTCR directly from the package.
tailbound.proportion    Proportions of specifyed subsets of clones.
top.cross               Perform sequential cross starting from the top
                        of a data frame.
top.fun                 Get samples from a repertoire slice-by-slice or
                        top-by-top and apply function to them.
twinsdata               Twins alpha-beta chain data
vis.clonal.dynamics     Visualise clonal dynamics among time points.
vis.clonal.space        Visualise occupied by clones homeostatic space
                        among Samples or groups.
vis.count.len           Plot a histogram of lengths.
vis.gene.usage          Histogram of segments usage.
vis.group.boxplot       Boxplot for groups of observations.
vis.heatmap             Heatmap.
vis.kmer.histogram      Plot of the most frequent kmers.
vis.logo                Logo - plots for amino acid and nucletide
                        profiles.
vis.number.count        Plot a histogram of counts.
vis.pca                 PCA result visualisation
vis.radarlike           Radar-like / spider-like plots.
vis.rarefaction         Rarefaction statistics visualisation.
vis.shared.clonotypes   Visualisation of shared clonotypes occurrences
                        among repertoires.
vis.top.proportions     Visualisation of top clones proportions.
