+,AbSeqCRep,AbSeqCRep-method
                        Combines 2 AbSeqCRep objects together for
                        comparison
+,AbSeqCRep,AbSeqRep-method
                        Combines a AbSeqCRep object with a AbSeqRep
                        object together for comparison
+,AbSeqRep,AbSeqCRep-method
                        Combines a AbSeqRep object with a AbSeqCRep
                        object together for comparison
+,AbSeqRep,AbSeqRep-method
                        Combines 2 AbSeqRep objects together for
                        comparison
.UTR5Analysis           5' UTR analysis
.abundanceAnalysis      Conducts abundance analysis
.abundancePlot          Abundance distribution
.alignQualityHeatMaps   Plots all 5 alignment quality heatmaps
.allPrimerNames         Collect primer names from FASTA
.aminoAcidBar           Plots amino acid composition logo
.aminoAcidPlot          Composition logo plot
.analyzeUpstreamValidity
                        Plots the validity of upstream sequences
.annotAnalysis          Annotation analysis
.asRepertoireAlignLen   Accessor for 'alignlen' slot
.asRepertoireBitscore   Accessor for 'bitscore' slot
.asRepertoireChain      Accessor for 'chain' slot
.asRepertoireDir        Accessor for the 'outdir' slot
.asRepertoireList       Accessor for AbSeqCRep's list of AbSeqRep
                        objects
.asRepertoireName       Accessor for the 'name' slot
.asRepertoirePrimer3    Accessor for the 'primer3end' slot
.asRepertoirePrimer5    Accessor for the 'primer5end' slot
.asRepertoireQueryStart
                        Accessor for 'qstart' slot
.asRepertoireSubjectStart
                        Accessor for 'sstart' slot
.asRepertoireUpstream   Accessor for the 'upstream' slot
.boxPlot                Creates a box plot
.calculateDInd          Calculates the "standard" diversity indices
.calculateDiversityEstimates
                        Calculates Lower Bound Estimates for unseen
                        species and Common Diversity Indices from
                        clonotype tables
.canonicalizeTitle      Convert file names to human friendly text
.capitalize             Helper function to capitalize the first letter
                        of 'str'
.checkVert              Checks if abseqPy has a metadata line that
                        suggests the orientation
.cloneDistHist          Marginal histogram of clonotypes (blue for
                        shared, grey for total). The y axis is scaled
                        by sqrt (but it doesn't really matter anyway,
                        since we're stripping away the y-ticks)
.cloneDistMarginal      Marginal density graph of clonotypes (blue for
                        shared, grey for total, purple for exclusive
                        clones)
.clonotypeAnalysis      Comprehensive clonotype analyses
.collateReports         Collate all HTML reports into a single
                        directory and cretate an entry 'index.html'
                        file that redirects to all collated HTML files
.commonPrimerNames      Collect the intersection of all primer names
                        within a collection of primer files
.correlationTest        Conducts pearson and spearman correlation
                        analysis on dataframe
.distanceMeasure        Computes the distance between pariwise samples
.diversityAnalysis      Title Diversity analysis
.emptyPlot              Creates and returns an empty plot
.findRepertoires        Given a directory =
                        <abseqPy_outputdir>/RESULT_DIR/, returns the
                        directories (repositories) in 'directory'. That
                        is, will not return any sample_vs_sample
                        directories. This is done by asserting that a
                        'repository' must have an (analysis.params)
                        file, and a summary.txt file.
.generateAllSpectratypes
                        Generates all FR/CDR spectratypes
.generateDelayedReport
                        Generates report for all samples in 'compare'
.generateReport         Generates HTML report from 'AbSeqRep' and
                        'AbSeqCRep' ojects
.getLineTypes           Helper function to return line types by
                        importance based on provided CD/Fs regions
.getTotal               Get total number of samples (n)
.hmFromMatrix           Plots a plotly heatmap from provided matrix
.inferAnalyzed          Returns all samples found under
                        'sampleDirectory'
.loadMatrixFromDF       Given a dataframe with the columns "from",
                        "to", and value.var, return a symmetric matrix
                        (with diagonal values = diag). I.e. a call to
                        isSymmetric(return_value_of_this_function) will
                        always be TRUE.
.loadSamplesFromString
                        Loads AbSeqCRep or AbSeqRep objects from a list
                        of sampleNames
.pairwiseComparison     Conduct all vs all pairwise comparison analyses
.plotCirclize           V-J association plot
.plotDist               Bar plotter
.plotDiversityCurves    Plots rarefaction, recapture, and de-dup plots
                        for specified 'region'
.plotDuplication        Duplication level plot
.plotErrorDist          Plots the error distribution for each region:
                        CDRs, FRs, IGV, IGD, and IGJ
.plotIGVErrors          Plots the error distribution for IGV germlines
.plotIGVUpstreamLenDist
                        Plot IGV family distribution for a given
                        'upstreamLengthRange'
.plotIGVUpstreamLenDistDetailed
                        Plots the detailed length distribution for IGV
                        families
.plotPrimerIGVStatus    Plots, for a given 'category' and 'pend', the
                        'primer' IGV indelled distribution in a bar
                        plot
.plotPrimerIntegrity    Plots the distribution of primer integrity for
                        a given 'category' and 5' or 3' 'pend'
.plotRarefaction        Rarefaction plot
.plotRecapture          Plots capture-recapture
.plotSamples            Monolith AbSeq Plot function - the "driver"
                        program
.plotSpectratype        Spectratype plotter
.plotUpstreamLength     Plot upstream distribution
.plotUpstreamLengthDist
                        Plot upstream sequence length distribution for
                        upstream sequences (5'UTR or secretion signal)
                        for a given 'upstreamLengthRange'
.primerAnalysis         Conducts primer specificity analysis
.prodDistPlot           Plots a distribution plot for different
                        productivity analysis files
.productivityAnalysis   Conducts productivty analysis
.productivityPlot       Summary of productivity
.readSummary            Return value specifed by key from AbSeq's
                        summary file
.regionAnalysis         Title Shows varying regions for a given
                        clonotype defined by its CDR3
.reportLBE              Reports abundance-based (Lower bound) diversity
                        estimates using the Vegan package
.saveAs                 Saves ggplot object as a Rdata file.
.scatterPlot            Title Creates a scatter plot
.scatterPlotComplex     Creates a complex scatter plot
.secretionSignalAnalysis
                        Secretion signal analysis
.substituteStringInFile
                        Substitutes the first occurance of 'key' with
                        'value' in 'filename'
.summarySE              Summary of dataframe
.topNDist               Title Clonotype table
.vennIntersection       Title Creates Venndiagram for clonotype
                        intersection
AbSeqCRep-class         S4 class - AbSeqCompositeRepertoire analysis
                        object
AbSeqRep-class          S4 class - AbSeqRepertoire analysis object
abseqReport             Visualize all analysis conducted by abseqPy
report                  Plots AbSeqRep or AbSeqCRep object to the
                        specfied directory
