patrickCNMartin/ChIPanalyser
ChIPanalyser: Predicting Transcription Factor Binding Sites

Package index
Search the patrickCNMartin/ChIPanalyser package
Vignettes
Functions
316
Source code
21
Man pages
134
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patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites
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API

API for patrickCNMartin/ChIPanalyser
ChIPanalyser: Predicting Transcription Factor Binding Sites

Global functions
.AccessExtract Source code
.ChIPScore Source code
.DNASequenceLength<-,genomicProfilesInternal,vector-method Man page
.GoFCheck Source code
.GoFLoci Source code
.GoFPred Source code
.IndexOfExistingSolution Source code
.OptimalFormatConversion Source code
.ZeroBackground,parameterOptions-method Man page
.ZeroBackground<-,parameterOptions,vector-method Man page
.allMetrics Source code
.averageExpPWMScore<-,genomicProfilesInternal,numeric-method Man page
.buildDatabase Source code
.cleanGoF Source code
.cleanUpAfterYourself Source code
.collapseParam Source code
.computeBPFrequency Source code
.computePWM Source code
.computePWMFromPFM Source code
.crossover Source code
.dispatchGraphical Source code
.drawBackground Source code
.drawCS Source code
.drawChIP Source code
.drawGeneRef Source code
.drawLegend Source code
.drawOccup Source code
.drawPrediction Source code
.drop<-,genomicProfilesInternal,vector-method Man page
.extractionChIP Source code
.fittyMacFitFace Source code
.formatCheck Source code
.generateChIPProfile Source code
.generateChIPProfileRcpp Source code
.generateNewPopulation Source code
.generatePWM,genomicProfilesInternal-method Man page
.generateRandomGASolution Source code
.genomicProfilesInternalContructor Source code
.geometricRatio Source code
.getGeneStarts Source code
.getIndexOfPWMThresholded Source code
.individualSurvival Source code
.initiateGASolutions Source code
.initiateSol Source code
.intMSE Source code
.internalChIPExtraction Source code
.internalChIPLoci Source code
.internalChIPLociSplit Source code
.internalChIPOccupValsLoci Source code
.internalChIPOccupValsParam Source code
.internalChIPParam Source code
.internalDNASequenceFromAccess Source code
.internalPWMScoreExt Source code
.internalUnlist Source code
.is.genomicProfiles Source code
.is.parameterOptions Source code
.lambdas Source code
.maxPWMScore<-,genomicProfilesInternal,vector-method Man page
.meanGoFScore Source code
.methodSwitchGoF Source code
.minPWMScore<-,genomicProfilesInternal,vector-method Man page
.mutate Source code
.optimalExtraction Source code
.paramTag,parameterOptions-method Man page
.paramTag<-,parameterOptions,character-method Man page
.parseJASPARPFM Source code
.parsePFM Source code
.parsePFMFromFile Source code
.parseRawPFM Source code
.parseTransfacPFM Source code
.peakExtractionFScore Source code
.peakParametersExt Source code
.populationFitness Source code
.prepCS Source code
.prepGR Source code
.prepLegend Source code
.profiles<-,genomicProfilesInternal,GRList-method Man page
.reorder Source code
.revert_to_class Source code
.scoreDNAStringSet Source code
.scoreReplace Source code
.setStrictSoltions Source code
.setfluxRangeSolutions Source code
.sigmoidWeight Source code
.splitRanges Source code
.tags,genomicProfilesInternal-method Man page
.tags<-,genomicProfilesInternal,character-method Man page
.unpackMetrics Source code
.updateGenomicProfiles Source code
.vectorSmooth Source code
.what.is.ChIPScore Source code
.what.is.chromatinState Source code
.what.is.geneRef Source code
.what.is.goodnessOfFit Source code
.what.is.occupancy Source code
.what.is.predictedProfile Source code
Access Man page
BPFrequency Man page
BPFrequency,genomicProfilesInternal-method Man page
BPFrequency-methods Man page
BPFrequency<- Man page
BPFrequency<-,genomicProfilesInternal,DNAStringSet-method Man page
BPFrequency<-,genomicProfilesInternal,vector-method Man page
BPFrequency<--methods Man page
ChIPScore-class Man page
ChIPanalyser Man page
ChIPanalyserData Man page
DNASequenceLength Man page
DNASequenceLength,genomicProfilesInternal-method Man page
DNASequenceLength-methods Man page
GRList-class Man page
PFMFormat Man page
PFMFormat,genomicProfilesInternal-method Man page
PFMFormat-methods Man page
PFMFormat<- Man page
PFMFormat<-,genomicProfilesInternal,character-method Man page
PFMFormat<--methods Man page
PWMThreshold Man page
PWMThreshold,parameterOptions-method Man page
PWMThreshold-methods Man page
PWMThreshold<- Man page
PWMThreshold<-,parameterOptions,numeric-method Man page
PWMThreshold<--methods Man page
PWMpseudocount Man page
PWMpseudocount,parameterOptions-method Man page
PWMpseudocount-methods Man page
PWMpseudocount<- Man page
PWMpseudocount<-,parameterOptions,numeric-method Man page
PWMpseudocount<--methods Man page
PositionFrequencyMatrix Man page
PositionFrequencyMatrix,genomicProfilesInternal-method Man page
PositionFrequencyMatrix-methods Man page
PositionFrequencyMatrix<- Man page
PositionFrequencyMatrix<-,genomicProfilesInternal,character-meth Man page
PositionFrequencyMatrix<-,genomicProfilesInternal,matrix-method Man page
PositionFrequencyMatrix<--methods Man page
PositionWeightMatrix Man page
PositionWeightMatrix,genomicProfilesInternal-method Man page
PositionWeightMatrix-methods Man page
PositionWeightMatrix<- Man page
PositionWeightMatrix<-,genomicProfilesInternal,matrix-method Man page
PositionWeightMatrix<--methods Man page
averageExpPWMScore Man page
averageExpPWMScore,genomicProfilesInternal-method Man page
averageExpPWMScore-methods Man page
backgroundSignal Man page
backgroundSignal,parameterOptions-method Man page
backgroundSignal-methods Man page
backgroundSignal<- Man page
backgroundSignal<-,parameterOptions,numeric-method Man page
backgroundSignal<--methods Man page
boundMolecules Man page
boundMolecules,parameterOptions-method Man page
boundMolecules-methods Man page
boundMolecules<- Man page
boundMolecules<-,parameterOptions,vector-method Man page
boundMolecules<--methods Man page
chip Man page
chipMean Man page
chipMean,parameterOptions-method Man page
chipMean-methods Man page
chipMean<- Man page
chipMean<-,parameterOptions,numeric-method Man page
chipMean<--methods Man page
chipSd Man page
chipSd,parameterOptions-method Man page
chipSd-methods Man page
chipSd<- Man page
chipSd<-,parameterOptions,numeric-method Man page
chipSd<--methods Man page
chipSmooth Man page
chipSmooth,parameterOptions-method Man page
chipSmooth-methods Man page
chipSmooth<- Man page
chipSmooth<-,parameterOptions,vector-method Man page
chipSmooth<--methods Man page
computeChIPProfile Man page Source code
computeGenomeWideScores Man page Source code
computeOccupancy Man page Source code
computeOptimal Man page Source code
computePWMScore Man page Source code
cs Man page
drop Man page
drop,genomicProfilesInternal-method Man page
drop-methods Man page
evolve Man page Source code
geneRef Man page
generateStartingPopulation Man page Source code
genomicProfiles Man page Source code
genomicProfiles-class Man page
genomicProfilesInternal-class Man page
getHighestFitnessSolutions Man page Source code
getTestingData Man page Source code
getTrainingData Man page Source code
initialize,ChIPScore-method Man page
initialize,genomicProfiles-method Man page
initialize,parameterOptions-method Man page
initialize-methods Man page
lambdaPWM Man page
lambdaPWM,parameterOptions-method Man page
lambdaPWM-methods Man page
lambdaPWM<- Man page
lambdaPWM<-,parameterOptions,vector-method Man page
lambdaPWM<--methods Man page
loci Man page
loci,ChIPScore-method Man page
loci-class Man page
loci-methods Man page
lociWidth Man page
lociWidth,parameterOptions-method Man page
lociWidth-methods Man page
lociWidth<- Man page
lociWidth<-,parameterOptions,numeric-method Man page
lociWidth<--methods Man page
maxPWMScore Man page
maxPWMScore,genomicProfilesInternal-method Man page
maxPWMScore-methods Man page
maxSignal Man page
maxSignal,parameterOptions-method Man page
maxSignal-methods Man page
maxSignal<- Man page
maxSignal<-,parameterOptions,numeric-method Man page
maxSignal<--methods Man page
minPWMScore Man page
minPWMScore,genomicProfilesInternal-method Man page
minPWMScore-methods Man page
naturalLog Man page
naturalLog,parameterOptions-method Man page
naturalLog-methods Man page
naturalLog<- Man page
naturalLog<-,parameterOptions,logical-method Man page
naturalLog<--methods Man page
noOfSites Man page
noOfSites,parameterOptions-method Man page
noOfSites-methods Man page
noOfSites<- Man page
noOfSites<-,parameterOptions,character-method Man page
noOfSites<-,parameterOptions,numeric-method Man page
noOfSites<--methods Man page
noiseFilter Man page
noiseFilter,parameterOptions-method Man page
noiseFilter-methods Man page
noiseFilter<- Man page
noiseFilter<-,parameterOptions,character-method Man page
noiseFilter<--methods Man page
nos-class Man page
parameterOptions Man page Source code
parameterOptions-class Man page
ploidy Man page
ploidy,parameterOptions-method Man page
ploidy-methods Man page
ploidy<- Man page
ploidy<-,parameterOptions,numeric-method Man page
ploidy<--methods Man page
plotOccupancyProfile Man page Source code
plotOptimalHeatMaps Man page Source code
processingChIP Man page Source code
profileAccuracyEstimate Man page Source code
profiles Man page
profiles,genomicProfilesInternal-method Man page
removeBackground Man page
removeBackground,parameterOptions-method Man page
removeBackground-methods Man page
removeBackground<- Man page
removeBackground<-,parameterOptions,vector-method Man page
removeBackground<--methods Man page
scores Man page
scores,ChIPScore-method Man page
scores-methods Man page
searchSites Man page Source code
setChromatinStates Man page Source code
show,ChIPScore-method Man page
show,genomicProfiles-method Man page
show,parameterOptions-method Man page
show-methods Man page
singleRun Man page Source code
splitData Man page Source code
stepSize Man page
stepSize,parameterOptions-method Man page
stepSize-methods Man page
stepSize<- Man page
stepSize<-,parameterOptions,numeric-method Man page
stepSize<--methods Man page
strandRule Man page
strandRule,parameterOptions-method Man page
strandRule-methods Man page
strandRule<- Man page
strandRule<-,parameterOptions,character-method Man page
strandRule<--methods Man page
top Man page
whichstrand Man page
whichstrand,parameterOptions-method Man page
whichstrand-methods Man page
whichstrand<- Man page
whichstrand<-,parameterOptions,character-method Man page
whichstrand<--methods Man page
patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.

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