API for shazam
Immunoglobulin Somatic Hypermutation Analysis
| Global functions | |
|---|---|
| .onAttach | Source code |
| A2_kM | Source code |
| A3_kMr | Source code |
| Baseline | Man page |
| Baseline-class | Man page |
| Baseline-method | Man page |
| CHARGE_MUTATIONS | Man page |
| DensityThreshold | Man page |
| DensityThreshold-class | Man page |
| DensityThreshold-method | Man page |
| GmmThreshold | Man page |
| GmmThreshold-class | Man page |
| GmmThreshold-method | Man page |
| HH_S1F | Man page |
| HH_S5F | Man page |
| HKL_S1F | Man page |
| HKL_S5F | Man page |
| HYDROPATHY_MUTATIONS | Man page |
| IMGT_SCHEMES | Man page |
| IMGT_V | Man page |
| IMGT_VDJ | Man page |
| IMGT_VDJ_BY_REGIONS | Man page |
| IMGT_V_BY_CODONS | Man page |
| IMGT_V_BY_REGIONS | Man page |
| IMGT_V_BY_SEGMENTS | Man page |
| IUPAC2nucs | Source code |
| MK_RS1NF | Man page |
| MK_RS5NF | Man page |
| MUTATION_SCHEMES | Man page |
| MutabilityModel | Man page |
| MutabilityModel-class | Man page |
| MutabilityModel-method | Man page |
| MutationDefinition | Man page |
| MutationDefinition-class | Man page |
| POLARITY_MUTATIONS | Man page |
| RegionDefinition | Man page |
| RegionDefinition-class | Man page |
| TargetingMatrix | Man page |
| TargetingMatrix-class | Man page |
| TargetingModel | Man page |
| TargetingModel-class | Man page |
| TargetingModel-method | Man page |
| U5N | Man page |
| VOLUME_MUTATIONS | Man page |
| _PACKAGE | Man page |
| allCodonMuts | Source code |
| allValidChars | Source code |
| analyzeMutations2NucUri | Source code |
| as.data.frame,MutabilityModel-method | Man page |
| avgSenSpc | Source code |
| baseline2DistPValue | Source code |
| baselineSigma | Source code |
| binMutationsByRegion | Source code |
| breakTiesHelper | Source code |
| calcBaseline | Man page |
| calcBaselineHelper | Source code |
| calcClonalConsensus | Source code |
| calcExpectedMutations | Man page Source code |
| calcObservedMutations | Man page Source code |
| calcTargetingDistance | Man page Source code |
| calculateMutability | Man page Source code |
| calculateMutationalPaths | Source code |
| calculateTargeting | Source code |
| canMutateTo | Source code |
| chars2Ambiguous | Source code |
| checkAmbiguousExist | Source code |
| collapseClones | Man page Source code |
| collapseMatrixToVector | Source code |
| computeCodonTable | Source code |
| computeMutationTypes | Source code |
| consensusSequence | Man page Source code |
| convertNumbering | Man page Source code |
| countNonNByRegion | Source code |
| createBaseline | Man page Source code |
| createMutabilityMatrix | Man page Source code |
| createMutationDefinition | Man page Source code |
| createRegionDefinition | Man page Source code |
| createSubstitutionMatrix | Man page Source code |
| createTargetingMatrix | Man page Source code |
| createTargetingModel | Man page Source code |
| dist5Mers | Source code |
| distToNearest | Man page Source code |
| editBaseline | Man page Source code |
| expectedMutations | Man page Source code |
| extendMutabilityMatrix | Man page Source code |
| extendSubstitutionMatrix | Man page Source code |
| findThreshold | Man page |
| findUniqSeq | Source code |
| getCharsInModel | Source code |
| getCloneRegion | Source code |
| getCodonNucs | Source code |
| getCodonNumb | Source code |
| getCodonPos | Source code |
| getContextInCodon | Source code |
| gmmFit | Source code |
| groupBaseline | Man page Source code |
| h.ucv | Source code |
| intersectPoint | Source code |
| kernel_fun_conv | Source code |
| kernel_fun_der | Source code |
| listMutations | Source code |
| listObservedMutations | Source code |
| makeAverage1merMut | Man page Source code |
| makeAverage1merSub | Man page Source code |
| makeDegenerate5merMut | Man page Source code |
| makeDegenerate5merSub | Man page Source code |
| makeGraphDf | Man page Source code |
| makeNullRegionDefinition | Source code |
| makeTargetingTestDb | Source code |
| minNumMutationsTune | Man page Source code |
| minNumSeqMutationsTune | Man page Source code |
| mixFunction | Source code |
| mutationType | Source code |
| mutationTypeOptimized | Source code |
| nearestDist | Source code |
| nonsquare5MerDist | Source code |
| nucs2IUPAC | Source code |
| observedMutations | Man page Source code |
| pairwise5MerDist | Source code |
| plot,Baseline,character-method | Man page |
| plot,DensityThreshold,missing-method | Man page |
| plot,GmmThreshold,missing-method | Man page |
| plot,TargetingModel,missing-method | Man page |
| plotBaselineDensity | Man page Source code |
| plotBaselineSummary | Man page Source code |
| plotDensityThreshold | Man page Source code |
| plotGmmThreshold | Man page Source code |
| plotJunctionAlignment | Source code |
| plotMutability | Man page Source code |
| plotSlideWindowTune | Man page Source code |
| plotTune | Man page Source code |
| print,DensityThreshold-method | Man page |
| print,GmmThreshold-method | Man page |
| print,MutabilityModel-method | Man page |
| removeCodonGaps | Source code |
| rescaleMutability | Source code |
| rocSpace | Source code |
| sampleMut | Source code |
| setRegionBoundaries | Man page Source code |
| shazam | Man page |
| shazam-package | Man page |
| shmulateSeq | Man page Source code |
| shmulateTree | Man page Source code |
| slideWindowDb | Man page Source code |
| slideWindowSeq | Man page Source code |
| slideWindowSeqHelper | Source code |
| slideWindowTune | Man page Source code |
| slideWindowTunePlot | Man page Source code |
| smoothValley | Source code |
| summarizeBaseline | Man page Source code |
| summary,Baseline-method | Man page |
| symmetrize | Source code |
| testBaseline | Man page Source code |
| toupperColumns | Source code |
| userDefineSenSpc | Source code |
| window5Mers | Source code |
| writeTargetingDistance | Man page Source code |
