Files in ChIPanalyser

ChIPanalyser: Predicting Transcription Factor Binding Sites

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

build/partial.rdb

data/ChIPanalyserData.rda

R/computeGenomeWide.R R/plotOccupancyDev.R R/4AllMethods.R R/DataPreprocessingGenericFunctionsDev.R R/GenomicProfileGenericFunctions.R R/DataPreprocessingDev.R R/profileAccuracyEstimateDev.R R/AllShowMethods.R R/computeChIPProfile.R R/plotOptimalHeatMapDev.R R/AllInitialize.R R/2AllS4Class_ProfileParameters.R R/computeOptimal.R R/parallelInternalFunctionsDev.R R/computeOccupancy.R R/3AllGenerics.R R/computePWMScore.R vignettes/ChIPanalyser.Rmd man/PositionFrequencyMatrix_--methods.Rd man/whichstrand-methods.Rd man/show-methods.Rd man/computeOptimal.Rd man/averageExpPWMScore.Rd man/naturalLog_--methods.Rd man/backgroundSignal_--methods.Rd man/PWMpseudocount-methods.Rd man/removeBackground-methods.Rd man/lambdaPWM_--methods.Rd man/PositionWeightMatrix_-.Rd man/lociWidth_--methods.Rd man/backgroundSignal-methods.Rd man/PFMFormat.Rd man/PWMpseudocount_-.Rd man/chipSmooth_--methods.Rd man/chipMean_--methods.Rd man/chipSd-methods.Rd man/lambdaPWM-methods.Rd man/scores.Rd man/loci-methods.Rd man/ChIPScore-class.Rd man/lambdaPWM.Rd man/chipSd_-.Rd man/removeBackground_--methods.Rd man/maxSignal.Rd man/noOfSites_--methods.Rd man/ploidy_-.Rd man/maxSignal-methods.Rd man/PFMFormat_--methods.Rd man/parameterOptions-class.Rd man/loci.Rd man/noiseFilter_--methods.Rd man/plotOccupancyProfile.Rd man/parameterOptions.Rd man/maxPWMScore-methods.Rd man/chipMean.Rd man/PWMpseudocount.Rd man/boundMolecules.Rd man/ploidy_--methods.Rd man/minPWMScore.Rd man/nos-class.Rd man/ChIPanalyser-package.Rd man/PositionWeightMatrix.Rd man/computePWMScore.Rd man/PFMFormat_.Rd man/noOfSites-methods.Rd man/chipSmooth_-.Rd man/chipMean-methods.Rd man/noOfSites_-.Rd man/strandRule_-.Rd man/lociWidth-methods.Rd man/noiseFilter_.Rd man/naturalLog-methods.Rd man/BPFrequency-methods.Rd man/strandRule.Rd man/boundMolecules_--methods.Rd man/DNASequenceLength-methods.Rd man/backgroundSignal.Rd man/genomicProfilesInternal-class.Rd man/stepSize_--methods.Rd man/PositionFrequencyMatrix-methods.Rd man/BPFrequency.Rd man/maxPWMScore.Rd man/lambdaPWM_.Rd man/stepSize.Rd man/noiseFilter.Rd man/strandRule-methods.Rd man/averageExpPWMScore-methods.Rd man/drop-methods.Rd man/drop.Rd man/scores-methods.Rd man/PWMThreshold.Rd man/boundMolecules_-.Rd man/PositionFrequencyMatrix.Rd man/BPFrequency_-.Rd man/data.Rd man/GRList-class.Rd man/removeBackground.Rd man/DNASequenceLength.Rd man/naturalLog.Rd man/computeChIPProfile.Rd man/ploidy-methods.Rd man/genomicProfiles-class.Rd man/PWMThreshold_-.Rd man/profiles-methods.Rd man/profileAccuracyEstimate.Rd man/noiseFilter-methods.Rd man/removeBackground_-.Rd man/naturalLog_-.Rd man/processingChIP.Rd man/BPFrequency_--methods.Rd man/PWMpseudocount_--methods.Rd man/whichstrand_--methods.Rd man/noOfSites.Rd man/chipMean_-.Rd man/initialize-methods.Rd man/maxSignal_-.Rd man/computeGenomeWideScores.Rd man/strandRule_--methods.Rd man/plotOptimalHeatMaps.Rd man/whichstrand_-.Rd man/PWMThreshold_--methods.Rd man/loci-class.Rd man/searchSites.Rd man/backgroundSignal_-.Rd man/ploidy.Rd man/PositionFrequencyMatrix_-.Rd man/maxSignal_--methods.Rd man/chipSd_--methods.Rd man/PositionWeightMatrix-methods.Rd man/chipSd.Rd man/stepSize-methods.Rd man/stepSize_-.Rd man/lociWidth.Rd man/genomicProfiles.Rd man/PositionWeightMatrix_--methods.Rd man/lociWidth_.Rd man/PWMThreshold-methods.Rd man/computeOccupancy.Rd man/chipSmooth.Rd man/minPWMScore-methods.Rd man/boundMolecules-methods.Rd man/PFMFormat-methods.Rd man/chipSmooth-methods.Rd man/whichstrand.Rd tests/runTests.R

inst/CITATION

inst/doc/ChIPanalyser.R inst/doc/ChIPanalyser.Rmd inst/doc/ChIPanalyser.pdf

inst/extdata/BCDSlx.pfm

inst/unitTests/genomeWideScoringAccess.rda

inst/unitTests/OccupancyAccess.rda

inst/unitTests/PWMScoreAccess.rda

inst/unitTests/GPPWithPFM.rda

inst/unitTests/test_Units.R

inst/unitTests/genomeWideScoringNoAccess.rda

inst/unitTests/PWMScoreNoAccess.rda

inst/unitTests/OccupancyNoAccess.rda

ChIPanalyser documentation built on Nov. 8, 2020, 8:23 p.m.