| AbSeqCRep-class | S4 class - AbSeqCompositeRepertoire analysis object |
| AbSeqRep-class | S4 class - AbSeqRepertoire analysis object |
| abseqReport | Visualize all analysis conducted by abseqPy |
| dot-abundanceAnalysis | Conducts abundance analysis |
| dot-abundancePlot | Abundance distribution |
| dot-alignQualityHeatMaps | Plots all 5 alignment quality heatmaps |
| dot-allPrimerNames | Collect primer names from FASTA |
| dot-aminoAcidBar | Plots amino acid composition logo |
| dot-aminoAcidPlot | Composition logo plot |
| dot-analyzeUpstreamValidity | Plots the validity of upstream sequences |
| dot-annotAnalysis | Annotation analysis |
| dot-asRepertoireAlignLen | Accessor for 'alignlen' slot |
| dot-asRepertoireBitscore | Accessor for 'bitscore' slot |
| dot-asRepertoireChain | Accessor for 'chain' slot |
| dot-asRepertoireDir | Accessor for the 'outdir' slot |
| dot-asRepertoireList | Accessor for AbSeqCRep's list of AbSeqRep objects |
| dot-asRepertoireName | Accessor for the 'name' slot |
| dot-asRepertoirePrimer3 | Accessor for the 'primer3end' slot |
| dot-asRepertoirePrimer5 | Accessor for the 'primer5end' slot |
| dot-asRepertoireQueryStart | Accessor for 'qstart' slot |
| dot-asRepertoireSubjectStart | Accessor for 'sstart' slot |
| dot-asRepertoireUpstream | Accessor for the 'upstream' slot |
| dot-boxPlot | Creates a box plot |
| dot-calculateDInd | Calculates the "standard" diversity indices |
| dot-calculateDiversityEstimates | Calculates Lower Bound Estimates for unseen species and... |
| dot-canonicalizeTitle | Convert file names to human friendly text |
| dot-capitalize | Helper function to capitalize the first letter of 'str' |
| dot-checkVert | Checks if abseqPy has a metadata line that suggests the... |
| dot-cloneDistHist | Marginal histogram of clonotypes (blue for shared, grey for... |
| dot-cloneDistMarginal | Marginal density graph of clonotypes (blue for shared, grey... |
| dot-clonotypeAnalysis | Comprehensive clonotype analyses |
| dot-collateReports | Collate all HTML reports into a single directory and cretate... |
| dot-commonPrimerNames | Collect the intersection of all primer names within a... |
| dot-correlationTest | Conducts pearson and spearman correlation analysis on... |
| dot-distanceMeasure | Computes the distance between pariwise samples |
| dot-diversityAnalysis | Title Diversity analysis |
| dot-emptyPlot | Creates and returns an empty plot |
| dot-findRepertoires | Given a directory = <abseqPy_outputdir>/RESULT_DIR/, returns... |
| dot-generateAllSpectratypes | Generates all FR/CDR spectratypes |
| dot-generateDelayedReport | Generates report for all samples in 'compare' |
| dot-generateReport | Generates HTML report from 'AbSeqRep' and 'AbSeqCRep' ojects |
| dot-getLineTypes | Helper function to return line types by importance based on... |
| dot-getTotal | Get total number of samples (n) |
| dot-hmFromMatrix | Plots a plotly heatmap from provided matrix |
| dot-inferAnalyzed | Returns all samples found under 'sampleDirectory' |
| dot-loadMatrixFromDF | Given a dataframe with the columns "from", "to", and... |
| dot-loadSamplesFromString | Loads AbSeqCRep or AbSeqRep objects from a list of... |
| dot-pairwiseComparison | Conduct all vs all pairwise comparison analyses |
| dot-plotCirclize | V-J association plot |
| dot-plotDist | Bar plotter |
| dot-plotDiversityCurves | Plots rarefaction, recapture, and de-dup plots for specified... |
| dot-plotDuplication | Duplication level plot |
| dot-plotErrorDist | Plots the error distribution for each region: CDRs, FRs, IGV,... |
| dot-plotIGVErrors | Plots the error distribution for IGV germlines |
| dot-plotIGVUpstreamLenDist | Plot IGV family distribution for a given... |
| dot-plotIGVUpstreamLenDistDetailed | Plots the detailed length distribution for IGV families |
| dot-plotPrimerIGVStatus | Plots, for a given 'category' and 'pend', the 'primer' IGV... |
| dot-plotPrimerIntegrity | Plots the distribution of primer integrity for a given... |
| dot-plotRarefaction | Rarefaction plot |
| dot-plotRecapture | Plots capture-recapture |
| dot-plotSamples | Monolith AbSeq Plot function - the "driver" program |
| dot-plotSpectratype | Spectratype plotter |
| dot-plotUpstreamLength | Plot upstream distribution |
| dot-plotUpstreamLengthDist | Plot upstream sequence length distribution for upstream... |
| dot-primerAnalysis | Conducts primer specificity analysis |
| dot-prodDistPlot | Plots a distribution plot for different productivity analysis... |
| dot-productivityAnalysis | Conducts productivty analysis |
| dot-productivityPlot | Summary of productivity |
| dot-readSummary | Return value specifed by key from AbSeq's summary file |
| dot-regionAnalysis | Title Shows varying regions for a given clonotype defined by... |
| dot-reportLBE | Reports abundance-based (Lower bound) diversity estimates... |
| dot-saveAs | Saves ggplot object as a Rdata file. |
| dot-scatterPlot | Title Creates a scatter plot |
| dot-scatterPlotComplex | Creates a complex scatter plot |
| dot-secretionSignalAnalysis | Secretion signal analysis |
| dot-substituteStringInFile | Substitutes the first occurance of 'key' with 'value' in... |
| dot-summarySE | Summary of dataframe |
| dot-topNDist | Title Clonotype table |
| dot-UTR5Analysis | 5' UTR analysis |
| dot-vennIntersection | Title Creates Venndiagram for clonotype intersection |
| plus-AbSeqCRep-AbSeqCRep-method | Combines 2 AbSeqCRep objects together for comparison |
| plus-AbSeqCRep-AbSeqRep-method | Combines a AbSeqCRep object with a AbSeqRep object together... |
| plus-AbSeqRep-AbSeqCRep-method | Combines a AbSeqRep object with a AbSeqCRep object together... |
| plus-AbSeqRep-AbSeqRep-method | Combines 2 AbSeqRep objects together for comparison |
| report | Plots AbSeqRep or AbSeqCRep object to the specfied directory |
