Files in patrickCNMartin/ChIPanalyserDev
ChIPanalyser: Predicting Transcription Factor Binding Sites
DESCRIPTION
NAMESPACE
NEWS
R/2AllS4Class_ProfileParameters.R
R/3AllGenerics.R
R/4AllMethods.R
R/AllInitialize.R
R/AllShowMethods.R
R/DataPreprocessingDev.R
R/DataPreprocessingGenericFunctionsDev.R
R/GenomicProfileGenericFunctions.R
R/computeChIPProfile.R
R/computeGenomeWide.R
R/computeOccupancy.R
R/computeOptimal.R
R/computePWMScore.R
R/parallelInternalFunctionsDev.R
R/plotOccupancyDev.R
R/plotOptimalHeatMapDev.R
R/profileAccuracyEstimateDev.R
README.md
annexeFunc/ChIPanalPerformAnalysis.R
annexeFunc/ChIPanalPerformAnalysis.sh
annexeFunc/ChipLoading.R
annexeFunc/performAnalysis.R
annexeFunc/submit.sh
data/ChIPanalyserData.rda
inst/CITATION
inst/extdata/BCDSlx.pfm
inst/unitTests/GPPWithPFM.rda
inst/unitTests/OccupancyAccess.rda
inst/unitTests/OccupancyNoAccess.rda
inst/unitTests/PWMScoreAccess.rda
inst/unitTests/PWMScoreNoAccess.rda
inst/unitTests/genomeWideScoringAccess.rda
inst/unitTests/genomeWideScoringNoAccess.rda
inst/unitTests/test_Units.R
man/BPFrequency-methods.Rd
man/BPFrequency.Rd
man/BPFrequency_--methods.Rd
man/BPFrequency_-.Rd
man/ChIPScore-class.Rd
man/ChIPanalyser-package.Rd
man/DNASequenceLength-methods.Rd
man/DNASequenceLength.Rd
man/GRList-class.Rd
man/PFMFormat-methods.Rd
man/PFMFormat.Rd
man/PFMFormat_--methods.Rd
man/PFMFormat_.Rd
man/PWMThreshold-methods.Rd
man/PWMThreshold.Rd
man/PWMThreshold_--methods.Rd
man/PWMThreshold_-.Rd
man/PWMpseudocount-methods.Rd
man/PWMpseudocount.Rd
man/PWMpseudocount_--methods.Rd
man/PWMpseudocount_-.Rd
man/PositionFrequencyMatrix-methods.Rd
man/PositionFrequencyMatrix.Rd
man/PositionFrequencyMatrix_--methods.Rd
man/PositionFrequencyMatrix_-.Rd
man/PositionWeightMatrix-methods.Rd
man/PositionWeightMatrix.Rd
man/PositionWeightMatrix_--methods.Rd
man/PositionWeightMatrix_-.Rd
man/averageExpPWMScore-methods.Rd
man/averageExpPWMScore.Rd
man/backgroundSignal-methods.Rd
man/backgroundSignal.Rd
man/backgroundSignal_--methods.Rd
man/backgroundSignal_-.Rd
man/boundMolecules-methods.Rd
man/boundMolecules.Rd
man/boundMolecules_--methods.Rd
man/boundMolecules_-.Rd
man/chipMean-methods.Rd
man/chipMean.Rd
man/chipMean_--methods.Rd
man/chipMean_-.Rd
man/chipSd-methods.Rd
man/chipSd.Rd
man/chipSd_--methods.Rd
man/chipSd_-.Rd
man/chipSmooth-methods.Rd
man/chipSmooth.Rd
man/chipSmooth_--methods.Rd
man/chipSmooth_-.Rd
man/computeChIPProfile.Rd
man/computeGenomeWideScores.Rd
man/computeOccupancy.Rd
man/computeOptimal.Rd
man/computePWMScore.Rd
man/data.Rd
man/drop-methods.Rd
man/drop.Rd
man/genomicProfiles-class.Rd
man/genomicProfiles.Rd
man/genomicProfilesInternal-class.Rd
man/initialize-methods.Rd
man/lambdaPWM-methods.Rd
man/lambdaPWM.Rd
man/lambdaPWM_--methods.Rd
man/lambdaPWM_.Rd
man/loci-class.Rd
man/loci-methods.Rd
man/loci.Rd
man/lociWidth-methods.Rd
man/lociWidth.Rd
man/lociWidth_--methods.Rd
man/lociWidth_.Rd
man/maxPWMScore-methods.Rd
man/maxPWMScore.Rd
man/maxSignal-methods.Rd
man/maxSignal.Rd
man/maxSignal_--methods.Rd
man/maxSignal_-.Rd
man/minPWMScore-methods.Rd
man/minPWMScore.Rd
man/naturalLog-methods.Rd
man/naturalLog.Rd
man/naturalLog_--methods.Rd
man/naturalLog_-.Rd
man/noOfSites-methods.Rd
man/noOfSites.Rd
man/noOfSites_--methods.Rd
man/noOfSites_-.Rd
man/noiseFilter-methods.Rd
man/noiseFilter.Rd
man/noiseFilter_--methods.Rd
man/noiseFilter_.Rd
man/nos-class.Rd
man/parameterOptions-class.Rd
man/parameterOptions.Rd
man/ploidy-methods.Rd
man/ploidy.Rd
man/ploidy_--methods.Rd
man/ploidy_-.Rd
man/plotOccupancyProfile.Rd
man/plotOptimalHeatMaps.Rd
man/processingChIP.Rd
man/profileAccuracyEstimate.Rd
man/profiles-methods.Rd
man/removeBackground-methods.Rd
man/removeBackground.Rd
man/removeBackground_--methods.Rd
man/removeBackground_-.Rd
man/scores-methods.Rd
man/scores.Rd
man/searchSites.Rd
man/show-methods.Rd
man/stepSize-methods.Rd
man/stepSize.Rd
man/stepSize_--methods.Rd
man/stepSize_-.Rd
man/strandRule-methods.Rd
man/strandRule.Rd
man/strandRule_--methods.Rd
man/strandRule_-.Rd
man/whichstrand-methods.Rd
man/whichstrand.Rd
man/whichstrand_--methods.Rd
man/whichstrand_-.Rd
tests/runTests.R
vignettes/.Rhistory
vignettes/ChIPanalyser.Rmd
vignettes/ChIPanalyser.pdf
