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 |
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