Package: ChIPanalyser 1.27.0

Patrick C.N. Martin

ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.

Authors:Patrick C.N.Martin & Nicolae Radu Zabet

ChIPanalyser_1.27.0.tar.gz
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ChIPanalyser.pdf |ChIPanalyser.html✨
ChIPanalyser/json (API)
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On BioConductor:ChIPanalyser-1.27.0(bioc 3.20)ChIPanalyser-1.26.0(bioc 3.19)

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bioconductor-package

74 exports 0.82 score 59 dependencies 1 mentions

Last updated 2 months agofrom:6ba9b03ff5

Exports:averageExpPWMScorebackgroundSignalbackgroundSignal<-boundMoleculesboundMolecules<-BPFrequencyBPFrequency<-chipMeanchipMean<-chipSdchipSd<-chipSmoothchipSmooth<-computeChIPProfilecomputeGenomeWideScorescomputeOccupancycomputeOptimalcomputePWMScoreDNASequenceLengthdropevolvegenerateStartingPopulationgenomicProfilesgetHighestFitnessSolutionsgetTestingDatagetTrainingDatainitializelambdaPWMlambdaPWM<-locilociWidthlociWidth<-maxPWMScoremaxSignalmaxSignal<-minPWMScorenaturalLognaturalLog<-noiseFilternoiseFilter<-noOfSitesnoOfSites<-parameterOptionsPFMFormatPFMFormat<-ploidyploidy<-plotOccupancyProfileplotOptimalHeatMapsPositionFrequencyMatrixPositionFrequencyMatrix<-PositionWeightMatrixPositionWeightMatrix<-processingChIPprofileAccuracyEstimateprofilesPWMpseudocountPWMpseudocount<-PWMThresholdPWMThreshold<-removeBackgroundremoveBackground<-scoressearchSitessetChromatinStatesshowsingleRunsplitDatastepSizestepSize<-strandRulestrandRule<-whichstrandwhichstrand<-

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsBSgenomecaToolscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgplotsgtoolshttrIRangesjsonliteKernSmoothlambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRcppRcppRollRCurlrestfulrRhtslibrjsonROCRRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc