| as.data.frame-method | S4 class defining a mutability model | 
| Baseline | S4 class defining a BASELINe (selection) object | 
| Baseline-class | S4 class defining a BASELINe (selection) object | 
| Baseline-method | S4 class defining a BASELINe (selection) object | 
| calcBaseline | Calculate the BASELINe PDFs (including for regions that include CDR3 and FWR4) | 
| 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 | 
| calculateMutability | Calculate total mutability | 
| CHARGE_MUTATIONS | Amino acid mutation definitions | 
| collapseClones | Constructs effective clonal sequences for all clones | 
| consensusSequence | Construct a consensus sequence | 
| convertNumbering | convertNumbering: IMGT-Kabat number conversion | 
| 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 | 
| DensityThreshold | Output of the 'dens' method of findThreshold | 
| DensityThreshold-class | Output of the 'dens' method of findThreshold | 
| DensityThreshold-method | Output of the 'dens' method of findThreshold | 
| distToNearest | Distance to nearest neighbor | 
| editBaseline | Edit the Baseline object | 
| expectedMutations | Calculate expected mutation frequencies | 
| extendMutabilityMatrix | Extends a mutability model to include Ns. | 
| extendSubstitutionMatrix | Extends a substitution model to include Ns. | 
| findThreshold | Find distance threshold | 
| GmmThreshold | Output of the 'gmm' method of findThreshold | 
| GmmThreshold-class | Output of the 'gmm' method of findThreshold | 
| GmmThreshold-method | Output of the 'gmm' method of findThreshold | 
| groupBaseline | Group BASELINe PDFs | 
| HH_S1F | Human heavy chain, silent, 1-mer, functional substitution model. | 
| HH_S5F | Human heavy chain, silent, 5-mer, functional targeting model. | 
| HKL_S1F | Human kappa and lambda chain, silent, 1-mer, functional substitution model. | 
| HKL_S5F | Human kappa and lambda light chain, silent, 5-mer, functional targeting model. | 
| HYDROPATHY_MUTATIONS | Amino acid mutation definitions | 
| IMGT_SCHEMES | IMGT unique numbering schemes | 
| IMGT_V | IMGT unique numbering schemes | 
| IMGT_VDJ | IMGT unique numbering schemes | 
| IMGT_VDJ_BY_REGIONS | IMGT unique numbering schemes | 
| IMGT_V_BY_CODONS | IMGT unique numbering schemes | 
| IMGT_V_BY_REGIONS | IMGT unique numbering schemes | 
| IMGT_V_BY_SEGMENTS | IMGT unique numbering schemes | 
| makeAverage1merMut | Make a 1-mer mutability model by averaging over a 5-mer mutability model | 
| makeAverage1merSub | Make a 1-mer substitution model by averaging over a 5-mer substitution model | 
| makeDegenerate5merMut | Make a degenerate 5-mer mutability model based on a 1-mer mutability model | 
| makeDegenerate5merSub | Make a degenerate 5-mer substitution model based on a 1-mer substitution model | 
| makeGraphDf | Build a data.frame from a ChangeoClone and an igraph object containing a clonal lineage | 
| minNumMutationsTune | Parameter tuning for minNumMutations | 
| minNumSeqMutationsTune | Parameter tuning for minNumSeqMutations | 
| MK_RS1NF | Mouse kappa chain, replacement and silent, 1-mer, non-functional substitution model. | 
| MK_RS5NF | Mouse kappa light chain, replacement and silent, 5-mer, non-functional targeting model. | 
| MutabilityModel | S4 class defining a mutability model | 
| MutabilityModel-class | S4 class defining a mutability model | 
| MutabilityModel-method | S4 class defining a mutability model | 
| MutationDefinition | S4 class defining replacement and silent mutation definitions | 
| MutationDefinition-class | S4 class defining replacement and silent mutation definitions | 
| MUTATION_SCHEMES | Amino acid mutation definitions | 
| observedMutations | Calculate observed numbers of mutations | 
| plot-method | S4 class defining a BASELINe (selection) object | 
| plot-method | Output of the 'dens' method of findThreshold | 
| plot-method | Output of the 'gmm' method of findThreshold | 
| plot-method | S4 class defining a targeting model | 
| plotBaselineDensity | Plots BASELINe probability density functions | 
| plotBaselineSummary | Plots BASELINe summary statistics | 
| plotDensityThreshold | Plot findThreshold results for the density method | 
| plotGmmThreshold | Plot findThreshold results for the gmm method | 
| plotMutability | Plot mutability probabilities | 
| plotSlideWindowTune | Visualize parameter tuning for sliding window approach | 
| plotTune | Visualize parameter tuning for minNumMutations and minNumSeqMutations | 
| POLARITY_MUTATIONS | Amino acid mutation definitions | 
| print-method | Output of the 'dens' method of findThreshold | 
| print-method | Output of the 'gmm' method of findThreshold | 
| print-method | S4 class defining a mutability model | 
| RegionDefinition | S4 class defining a region definition | 
| RegionDefinition-class | S4 class defining a region definition | 
| setRegionBoundaries | Build a RegionDefinition object that includes CDR3 and FWR4. | 
| shazam | The shazam package | 
| shmulateSeq | Simulate mutations in a single sequence | 
| shmulateTree | Simulate mutations in a lineage tree | 
| slideWindowDb | Sliding window approach towards filtering sequences in a 'data.frame' | 
| slideWindowSeq | Sliding window approach towards filtering a single sequence | 
| slideWindowTune | Parameter tuning for sliding window approach | 
| slideWindowTunePlot | slideWindowTunePlot - plotSlideWindowTune backward compatability | 
| summarizeBaseline | Calculate BASELINe summary statistics | 
| summary-method | S4 class defining a BASELINe (selection) object | 
| TargetingMatrix | S4 class defining a targeting matrix | 
| TargetingMatrix-class | S4 class defining a targeting matrix | 
| TargetingModel | S4 class defining a targeting model | 
| TargetingModel-class | S4 class defining a targeting model | 
| TargetingModel-method | S4 class defining a targeting model | 
| testBaseline | Two-sided test of BASELINe PDFs | 
| U5N | Uniform 5-mer null targeting model. | 
| VOLUME_MUTATIONS | Amino acid mutation definitions | 
| writeTargetingDistance | Write targeting model distances to a file |