API for shazam
Immunoglobulin Somatic Hypermutation Analysis

Global functions
Baseline Man page
Baseline-class Man page
CHARGE_MUTATIONS Man page
DensityThreshold Man page
DensityThreshold-class Man page
DensityThreshold-method Man page Man page
GmmThreshold Man page
GmmThreshold-class Man page
GmmThreshold-method Man page 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_V_BY_REGIONS Man page
IUPAC2nucs Source code
MK_RS1NF Man page
MK_RS5NF Man page
MUTATION_SCHEMES Man page
MutationDefinition Man page
MutationDefinition-class Man page
POLARITY_MUTATIONS Man page
PowersOfTwo Source code
RegionDefinition Man page
RegionDefinition-class Man page
TargetingModel Man page
TargetingModel-class Man page
U5N Man page
VOLUME_MUTATIONS Man page
allCodonMuts Source code
allValidChars Source code
analyzeMutations2NucUri Source code
avgSenSpc Source code
baseline2DistPValue Source code
baselineCI Source code
baselinePValue Source code
baselineSigma Source code
binMutationsByRegion Source code
break2chunks Source code
breakTiesHelper Source code
calcBaseline Man page Source code
calcBaselineBinomialPdf Source code
calcBaselineHelper Source code
calcClonalConsensus Source code
calcClonalConsensusHelper Source code
calcExpectedMutations Man page Source code
calcObservedMutations Man page Source code
calcTargetingDistance Man page Source code
calculateMutationalPaths Source code
calculateTargeting Source code
calculate_bayesGHelper Source code
canMutateTo Source code
chars2Ambiguous Source code
checkColumns Source code
clearConsole Man page Source code
collapseClones Man page Source code
collapseMatrixToVector Source code
combineWeightedPosteriors Source code
computeCodonTable Source code
computeMutationTypes Source code
convolutionPowersOfTwo Source code
convolutionPowersOfTwoByTwos 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
fastConv Source code
findThreshold Man page Source code
findUniqSeq Source code
gammaArea Source code
getBaseTheme Source code
getBaselineStats Man page Source code
getCharsInModel Source code
getCodonNucs Source code
getCodonNumb Source code
getCodonPos Source code
getContextInCodon Source code
getPlatform Man page Source code
getnproc Man page Source code
gmmFit Source code
groupBaseline Man page Source code
groupPosteriors Source code
intersectPoint 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
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
normArea Source code
nucs2IUPAC Source code
observedMutations Man page Source code
pairwise5MerDist Source code
plot,DensityThreshold,missing-method Man page
plot,GmmThreshold,missing-method Man page
plotBaselineDensity Man page Source code
plotBaselineSummary Man page Source code
plotDensityThreshold Man page Source code
plotGmmThreshold Man page Source code
plotMutability Man page Source code
plotTune Man page Source code
print,DensityThreshold-method Man page
print,GmmThreshold-method Man page
progressBar Source code
removeCodonGaps Source code
rescaleMutability Source code
rocSpace Source code
sampleMut 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
symmetrize Source code
testBaseline Man page Source code
toupperColumns Source code
translateCodonToAminoAcid Source code
userDefineSenSpc Source code
weighted_conv Source code
window5Mers Source code
writeTargetingDistance Man page Source code
shazam documentation built on July 4, 2017, 9:43 a.m.