ABBREV_AA               Amino acid abbreviation translations
AbundanceCurve-class    S4 class defining a clonal abundance curve
ChangeoClone-class      S4 class defining a clone
DEFAULT_COLORS          Default colors
DiversityCurve-class    S4 class defining a diversity curve
EdgeTest-class          S4 class defining edge significance
Example10x              Small example 10x Genomics Ig V(D)J sequences
                        from CD19+ B cells isolated from PBMCs of a
                        healthy human donor. Down-sampled from data
                        provided by 10x Genomics under a Creative
                        Commons Attribute license, and processed with
                        their Cell Ranger pipeline.
ExampleDb               Example AIRR database
ExampleDbChangeo        Example Change-O database
ExampleTrees            Example Ig lineage trees
IMGT_REGIONS            IMGT V-segment regions
IUPAC_CODES             IUPAC ambiguous characters
MRCATest-class          S4 class defining edge significance
SingleDb                Single sequence AIRR database
alakazam                The Alakazam package
aliphatic               Calculates the aliphatic index of amino acid
                        sequences
alphaDiversity          Calculate clonal alpha diversity
aminoAcidProperties     Calculates amino acid chemical properties for
                        sequence data
baseTheme               Standard ggplot settings
buildPhylipLineage      Infer an Ig lineage using PHYLIP
bulk                    Calculates the average bulkiness of amino acid
                        sequences
calcCoverage            Calculate sample coverage
calcDiversity           Calculate the diversity index
charge                  Calculates the net charge of amino acid
                        sequences.
checkColumns            Check data.frame for valid columns and issue
                        message if invalid
collapseDuplicates      Remove duplicate DNA sequences and combine
                        annotations
combineIgphyml          Combine IgPhyML object parameters into a
                        dataframe
countClones             Tabulates clones sizes
countGenes              Tabulates V(D)J allele, gene or family usage
                        within each locus.
countPatterns           Count sequence patterns
cpuCount                Available CPU cores
estimateAbundance       Estimates the complete clonal relative
                        abundance distribution
extractVRegion          Extracts FWRs and CDRs from IMGT-gapped
                        sequences
getAAMatrix             Build an AA distance matrix
getDNAMatrix            Build a DNA distance matrix
getMRCA                 Retrieve the first non-root node of a lineage
                        tree
getPathLengths          Calculate path lengths from the tree root
getPositionQuality      Get a data.frame with sequencing qualities per
                        position
getSegment              Get Ig segment allele, gene and family names
graphToPhylo            Convert a tree in igraph 'graph' format to ape
                        'phylo' format.
gravy                   Calculates the hydrophobicity of amino acid
                        sequences
gridPlot                Plot multiple ggplot objects
groupGenes              Group sequences by gene assignment
isValidAASeq            Validate amino acid sequences
junctionAlignment       Calculate junction region alignment properties
makeChangeoClone        Generate a ChangeoClone object for lineage
                        construction
makeTempDir             Create a temporary folder
maskPositionsByQuality
                        Mask sequence positions with low quality
maskSeqEnds             Masks ragged leading and trailing edges of
                        aligned DNA sequences
maskSeqGaps             Masks gap characters in DNA sequences
nonsquareDist           Calculate pairwise distances between sequences
padSeqEnds              Pads ragged ends of aligned DNA sequences
pairwiseDist            Calculate pairwise distances between sequences
pairwiseEqual           Calculate pairwise equivalence between
                        sequences
permuteLabels           Permute the node labels of a tree
phyloToGraph            Convert a tree in ape 'phylo' format to igraph
                        'graph' format.
plotAbundanceCurve      Plot a clonal abundance distribution
plotDiversityCurve      Plot the results of alphaDiversity
plotDiversityTest       Plot the results of diversity testing
plotEdgeTest            Plot the results of an edge permutation test
plotMRCATest            Plot the results of a founder permutation test
plotSubtrees            Plots subtree statistics for multiple trees
polar                   Calculates the average polarity of amino acid
                        sequences
progressBar             Standard progress bar
rarefyDiversity         Generate a clonal diversity index curve
readChangeoDb           Read a Change-O tab-delimited database file
readFastqDb             Load sequencing quality scores from a FASTQ
                        file
readIgphyml             Read in output from IgPhyML
seqDist                 Calculate distance between two sequences
seqEqual                Test DNA sequences for equality.
sortGenes               Sort V(D)J genes
stoufferMeta            Weighted meta-analysis of p-values via
                        Stouffer's method
summarizeSubtrees       Generate subtree summary statistics for a tree
tableEdges              Tabulate the number of edges between
                        annotations within a lineage tree
testDiversity           Pairwise test of the diversity index
testEdges               Tests for parent-child annotation enrichment in
                        lineage trees
testMRCA                Tests for MRCA annotation enrichment in lineage
                        trees
translateDNA            Translate nucleotide sequences to amino acids
translateStrings        Translate a vector of strings
writeChangeoDb          Write a Change-O tab-delimited database file
