Baseline-class          S4 class defining a BASELINe (selection) object
HS1FDistance            Human single nucleotide distance matrix.
HS5FModel               Human 5-mer targeting model.
IMGT_SCHEMES            IMGT unique numbering schemes
InfluenzaDb             Example Change-O database
M1NDistance             Mouse single nucleotide distance matrix.
MUTATION_SCHEMES        Amino acid mutation definitions
MutationDefinition-class
                        S4 class defining replacement and silent
                        mutation definitions
RegionDefinition-class
                        S4 class defining a region definition
TargetingModel-class    S4 class defining a targeting model
U5NModel                Uniform 5-mer targeting model.
calcBaseline            Calculate the BASELINe PDFs
calcDBExpectedMutations
                        Calculate expected mutation frequencies
calcDBObservedMutations
                        Calculate observed numbers of mutations
calcExpectedMutations   Calculate expected mutation frequencies of a
                        sequence
calcObservedMutations   Count the number of observed mutations in a
                        sequence.
calcTargetingDistance   Calculates a 5-mer distance matrix from a
                        TargetingModel object
clearConsole            Clears the console
collapseByClone         Identifies clonal consensus sequences
createBaseline          Creates a Baseline object
createMutabilityMatrix
                        Builds a mutability model
createMutationDefinition
                        Creates a MutationDefinition
createRegionDefinition
                        Creates a RegionDefinition
createSubstitutionMatrix
                        Builds a substitution model
createTargetingMatrix   Calculates a targeting rate matrix
createTargetingModel    Creates a TargetingModel
distToNearest           Distance to nearest neighbor
extendMutabilityMatrix
                        Extends a mutability model to include Ns.
extendSubstitutionMatrix
                        Extends a substitution model to include Ns.
getBaselineStats        Gets the summary statistics of a Baseline
                        object
getPlatform             Determines the OS platform being used
getnproc                Determines the numbers of CPU cores available
groupBaseline           Group BASELINe PDFs
plotBaselineDensity     Plots BASELINe probability density functions
plotBaselineSummary     Plots BASELINe summary statistics
plotMutability          Plot mutability probabilities
shazam                  The shazam package
summarizeBaseline       Calculate BASELINe summary statistics
writeTargetingDistance
                        Write targeting model distances to a file
