ABBREV_AA               Amino acid abbreviation translations
ChangeoClone-class      S4 class defining a clone
DEFAULT_COLORS          Default colors
DiversityCurve-class    S4 class defining diversity curve
DiversityTest-class     S4 class defining diversity significance
ExampleTrees            Example Ig lineage trees
IMGT_REGIONS            IMGT V-segment regions
IUPAC_CODES             IUPAC ambiguous characters
alakazam                The alakazam package
aliphatic               Calculates the aliphatic index of amino acid
                        sequences
aminoAcidProperties     Calculates amino acid chemical properties for
                        sequence data
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.
collapseDuplicates      Remove duplicate DNA sequences and combine
                        annotations
countClones             Tabulates clones sizes
countGenes              Tabulates V(D)J allele, gene or family usage.
countPatterns           Count sequence patterns
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
getSegment              Get Ig segment allele, gene and family names
getSeqDistance          Calculate distance between two sequences
getSeqMatrix            Calculate pairwise distances between sequences
gravy                   Calculates the hydrophobicity of amino acid
                        sequences
isValidAASeq            Validate amino acid sequences
makeChangeoClone        Generate a ChangeoClone object for lineage
                        construction
makeTempDir             Create a temporary folder
maskSeqEnds             Masks ragged leading and trailing edges of
                        aligned DNA sequences
maskSeqGaps             Masks gap characters in DNA sequences
multiggplot             Plot multiple ggplot objects
plotAbundance           Plots a clonal abundance distribution
plotDiversityCurve      Plot the results of rarefyDiversity
polar                   Calculates the average polarity of amino acid
                        sequences
rarefyDiversity         Generate a clonal diversity index curve
readChangeoDb           Read a Change-O tab-delimited database file
stoufferMeta            Weighted meta-analysis of p-values via
                        Stouffer's method
testDiversity           Pairwise test of the diversity index
testSeqEqual            Test DNA sequences for equality.
translateDNA            Translate nucleotide sequences to amino acids
translateStrings        Translate a vector of strings
writeChangeoDb          Write a Change-O tab-delimited database file
