Package: ChIPanalyser 1.29.0

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

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ChIPanalyser.pdf |ChIPanalyser.html✨
ChIPanalyser/json (API)
NEWS

# Install 'ChIPanalyser' in R:
install.packages('ChIPanalyser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Access - ChIPanalyserData
  • chip - ChIPanalyserData
  • cs - ChIPanalyserData
  • geneRef - ChIPanalyserData
  • top - ChIPanalyserData

On BioConductor:ChIPanalyser-1.29.0(bioc 3.21)ChIPanalyser-1.28.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarebiologicalquestionworkflowsteptranscriptionsequencingchiponchipcoveragealignmentchipseqsequencematchingdataimportpeakdetection

4.34 score 11 scripts 244 downloads 1 mentions 74 exports 60 dependencies

Last updated 1 months agofrom:0c32095953. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

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.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgplotsgtoolshttrIRangesjsonliteKernSmoothlambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRcppRcppRollRCurlrestfulrRhtslibrjsonROCRRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

The ChIPanalyser User's Guide

Patrick Martin

Rendered fromChIPanalyser.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-09-02
Started: 2017-08-24

The ChIPanalyser User's Guide

Patrick Martin

Rendered fromGA_ChIPanalyser.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-09-02
Started: 2022-09-02

Readme and manuals

Help Manual

Help pageTopics
ChIPanalyser: Predicting Transcription Factor Binding SitesChIPanalyser
Accessor for 'averageExpPWMScore' slot in a 'genomicProfiles' object.averageExpPWMScore
~~ Methods for Function 'averageExpPWMScore' ~~averageExpPWMScore-methods
Accessor method for the 'backgroundSignal' slot in a 'parameterOptions' object.backgroundSignal
~~ Methods for Function 'backgroundSignal' ~~backgroundSignal-methods
Setter method for 'backgroundSignal' slot in a 'parameterOptions'backgroundSignal<-
~~ Methods for Function 'backgroundSignal<-' ~~backgroundSignal<--methods
Accessor methods for 'boundMolecules' slot in 'parameterOptions' object.boundMolecules
~~ Methods for Function 'boundMolecules' ~~boundMolecules-methods
Setter method for the 'boundMolecules' slot in a 'parameterOptions' object.boundMolecules<-
~~ Methods for Function 'boundMolecules<-' ~~boundMolecules<--methods
Accessor method for 'BPFrequency' slot in a 'genomicProfiles' object.BPFrequency
~~ Methods for Function 'BPFrequency' ~~BPFrequency-methods
Setter method for 'BPFrequency' slot in a 'genomicProfiles' object.BPFrequency<-
~~ Methods for Function 'BPFrequency<-' ~~BPFrequency<--methods
ChIPanalyserDataAccess chip ChIPanalyserData cs geneRef top
Accessor method for 'chipMean' slot in a 'parameterOptions' object.chipMean
~~ Methods for Function 'chipMean' ~~chipMean-methods
Access methods for 'chipMean' slot in 'parameterOptions' object.chipMean<-
~~ Methods for Function 'chipMean<-' ~~chipMean<--methods
Class '"ChIPScore"'ChIPScore-class loci,ChIPScore-method scores,ChIPScore-method
Accessor method for 'chipSd' slot in a 'parameterOptions' object.chipSd
~~ Methods for Function 'chipSd' ~~chipSd-methods
Setter methods for 'chipSd' slot in a 'parameterOptions' object.chipSd<-
~~ Methods for Function 'chipSd<-' ~~chipSd<--methods
Accessor methods for 'chipSmooth' slot in a 'parameterOptions' object.chipSmooth
~~ Methods for Function 'chipSmooth' ~~chipSmooth-methods
Setter method for 'chipSmooth' slot in 'parameterOptions' object.chipSmooth<-
~~ Methods for Function 'chipSmooth<-' ~~chipSmooth<--methods
Computing ChIP-seq like profiles from Occupancy data.computeChIPProfile
Computing Genome Wide scorescomputeGenomeWideScores
Compute Occupancy values from PWM Scores based on model.computeOccupancy
compute Optimal ParameterscomputeOptimal
Compute PWM Scores of sites above threshold.computePWMScore
Accessor method for 'DNASequenceLength' slot in a 'genomicProfiles'DNASequenceLength
~~ Methods for Function 'DNASequenceLength' ~~DNASequenceLength-methods
Accessor Method for the 'drop' slot in a 'genomicProfiles' object.drop
~~ Methods for Function 'drop' ~~drop-methods
Running the ChIPanalyser implementation of a Genetic algorithm.evolve
Generate Starting population for ChIPanalyser Genetic algortihmgenerateStartingPopulation
Genomic Profile objectgenomicProfiles
Class '"genomicProfiles"'genomicProfiles-class
Class '"genomicProfilesInternal"'.averageExpPWMScore<-,genomicProfilesInternal,numeric-method .DNASequenceLength<-,genomicProfilesInternal,vector-method .drop<-,genomicProfilesInternal,vector-method .generatePWM,genomicProfilesInternal-method .maxPWMScore<-,genomicProfilesInternal,vector-method .minPWMScore<-,genomicProfilesInternal,vector-method .profiles<-,genomicProfilesInternal,GRList-method .tags,genomicProfilesInternal-method .tags<-,genomicProfilesInternal,character-method averageExpPWMScore,genomicProfilesInternal-method BPFrequency,genomicProfilesInternal-method BPFrequency<-,genomicProfilesInternal,DNAStringSet-method BPFrequency<-,genomicProfilesInternal,vector-method DNASequenceLength,genomicProfilesInternal-method drop,genomicProfilesInternal-method genomicProfilesInternal-class maxPWMScore,genomicProfilesInternal-method minPWMScore,genomicProfilesInternal-method PFMFormat,genomicProfilesInternal-method PFMFormat<-,genomicProfilesInternal,character-method PositionFrequencyMatrix,genomicProfilesInternal-method PositionFrequencyMatrix<-,genomicProfilesInternal,character-method PositionFrequencyMatrix<-,genomicProfilesInternal,matrix-method PositionWeightMatrix,genomicProfilesInternal-method PositionWeightMatrix<-,genomicProfilesInternal,matrix-method profiles,genomicProfilesInternal-method
Get Highest Fitness SolutionsgetHighestFitnessSolutions
Extract testing data from ChIPscore objectgetTestingData
Extract training data from ChIPscore objectgetTrainingData
Class '"GRList"'GRList-class
~~ Methods for Function 'initialize' ~~initialize,ChIPScore-method initialize,genomicProfiles-method initialize,parameterOptions-method initialize-methods
Accessor Method for the 'lambdaPWM' slot in a 'parameterOptions' objectlambdaPWM
~~ Methods for Function 'lambdaPWM' ~~lambdaPWM-methods
Setter Method for the 'lambdaPWM' slot in a 'parameterOptions' objectlambdaPWM<-
~~ Methods for Function 'lambdaPWM<-' ~~lambdaPWM<--methods
Accessor Method for the 'loci' slot in a 'ChIPScore' objectloci
Class '"loci"'loci-class
~~ Methods for Function 'loci' ~~loci-methods
Accessor Method for the 'lociWidth' slot in a 'parameterOptions' objectlociWidth
~~ Methods for Function 'lociWidth' ~~lociWidth-methods
Setter Method for the 'lociWidth' slot in a 'parameterOptions' objectlociWidth<-
~~ Methods for Function 'lociWidth<-' ~~lociWidth<--methods
Accessor function for 'maxPWMScore' slot in a 'genomicProfiles' object.maxPWMScore
~~ Methods for Function 'maxPWMScore' ~~maxPWMScore-methods
Accessor method for the 'maxSignal' slot in a 'parameterOptions' object.maxSignal
~~ Methods for Function 'maxSignal' ~~maxSignal-methods
Setter method for 'maxSignal' slot in a 'parameterOptions' object.maxSignal<-
~~ Methods for Function 'maxSignal<-' ~~maxSignal<--methods
Accessor method the 'minPWMScore' slot in a 'genomicProfiles' objectminPWMScore
~~ Methods for Function 'minPWMScore' ~~minPWMScore-methods
Accessor method the 'naturalLog' slot in a 'parameterOptions' object.naturalLog
~~ Methods for Function 'naturalLog' ~~naturalLog-methods
Setter method for the 'naturalLog' slot in a 'parameterOptions' object.naturalLog<-
~~ Methods for Function 'naturalLog<-' ~~naturalLog<--methods
Accessor Method for the 'noiseFilter' slot in a 'parameterOptions' objectnoiseFilter
~~ Methods for Function 'noiseFilter' ~~noiseFilter-methods
Setter Method for the 'noiseFilter' slot in a 'parameterOptions' objectnoiseFilter<-
~~ Methods for Function 'noiseFilter<-' ~~noiseFilter<--methods
Accessor Method for the 'noOfSites' slot in a 'parameterOptions' objectnoOfSites
~~ Methods for Function 'noOfSites' ~~noOfSites-methods
Setter Method for the 'noOfSites' slot in a 'parameterOptions' object.noOfSites<-
~~ Methods for Function 'noOfSites<-' ~~noOfSites<--methods
Class '"nos"'nos-class
parameter Options objectparameterOptions
Class '"parameterOptions"'.paramTag,parameterOptions-method .paramTag<-,parameterOptions,character-method .ZeroBackground,parameterOptions-method .ZeroBackground<-,parameterOptions,vector-method backgroundSignal,parameterOptions-method backgroundSignal<-,parameterOptions,numeric-method boundMolecules,parameterOptions-method boundMolecules<-,parameterOptions,vector-method chipMean,parameterOptions-method chipMean<-,parameterOptions,numeric-method chipSd,parameterOptions-method chipSd<-,parameterOptions,numeric-method chipSmooth,parameterOptions-method chipSmooth<-,parameterOptions,vector-method lambdaPWM,parameterOptions-method lambdaPWM<-,parameterOptions,vector-method lociWidth,parameterOptions-method lociWidth<-,parameterOptions,numeric-method maxSignal,parameterOptions-method maxSignal<-,parameterOptions,numeric-method naturalLog,parameterOptions-method naturalLog<-,parameterOptions,logical-method noiseFilter,parameterOptions-method noiseFilter<-,parameterOptions,character-method noOfSites,parameterOptions-method noOfSites<-,parameterOptions,character-method noOfSites<-,parameterOptions,numeric-method parameterOptions-class ploidy,parameterOptions-method ploidy<-,parameterOptions,numeric-method PWMpseudocount,parameterOptions-method PWMpseudocount<-,parameterOptions,numeric-method PWMThreshold,parameterOptions-method PWMThreshold<-,parameterOptions,numeric-method removeBackground,parameterOptions-method removeBackground<-,parameterOptions,vector-method stepSize,parameterOptions-method stepSize<-,parameterOptions,numeric-method strandRule,parameterOptions-method strandRule<-,parameterOptions,character-method whichstrand,parameterOptions-method whichstrand<-,parameterOptions,character-method
Accesor method for the 'PFMFormat' slot in a 'genomicProfiles' objectPFMFormat
~~ Methods for Function 'PFMFormat' ~~PFMFormat-methods
Setter method for the 'PFMFormat' slot in a 'genomicProfiles' objectPFMFormat<-
~~ Methods for Function 'PFMFormat<-' ~~PFMFormat<--methods
Accessor method for the 'ploidy' slot in a 'parameterOptions' objectploidy
~~ Methods for Function 'ploidy' ~~ploidy-methods
Setter Method for the 'ploidy' slot in an 'parameterOptions' objectploidy<-
~~ Methods for Function 'ploidy<-' ~~ploidy<--methods
Plot Occupancy ProfilesplotOccupancyProfile
Heat Map of optimal ParametersplotOptimalHeatMaps
Accessor method for the 'PFM' slot in a 'genomicProfiles' objectPositionFrequencyMatrix
~~ Methods for Function 'PositionFrequencyMatrix' ~~PositionFrequencyMatrix-methods
Setter method for the 'PFM' slot in a 'genomicProfiles' objectPositionFrequencyMatrix<-
~~ Methods for Function 'PositionFrequencyMatrix<-' ~~PositionFrequencyMatrix<--methods
Accessor Method for the 'PWM' slot in a 'genomicProfiles' objectPositionWeightMatrix
~~ Methods for Function 'PositionWeightMatrix' ~~PositionWeightMatrix-methods
Setter Method for the 'PositionWeightMatrix' slot in a 'genomicProfiles' objectPositionWeightMatrix<-
~~ Methods for Function 'PositionWeightMatrix<-' ~~PositionWeightMatrix<--methods
Pre-processing ChIP-seq dataprocessingChIP
Estimating Accuracy of predicted ProfilesprofileAccuracyEstimate
~~ Methods for Function 'profiles' ~~profiles
Accessor Method for a 'PWMpseudocount' slot in a 'parameterOptions'PWMpseudocount
~~ Methods for Function 'PWMpseudocount' ~~PWMpseudocount-methods
Setter Method for the 'pseudocount' slot in a 'parameterOptions' objectPWMpseudocount<-
~~ Methods for Function 'PWMpseudocount<-' ~~PWMpseudocount<--methods
Accessor method for the 'PWMThreshold' slot in a 'parameterOptions' objectPWMThreshold
~~ Methods for Function 'PWMThreshold' ~~PWMThreshold-methods
Setter Method for the 'PWMThreshold' slot in a 'parameterOptions' objectPWMThreshold<-
~~ Methods for Function 'PWMThreshold<-' ~~PWMThreshold<--methods
Accessor Method for the 'removeBackground' slot in a 'parameterOptions' objectremoveBackground
~~ Methods for Function 'removeBackground' ~~removeBackground-methods
Setter Method for the 'removeBackground' slot in a 'parameterOptions' objectremoveBackground<-
~~ Methods for Function 'removeBackground<-' ~~removeBackground<--methods
Accessor Method for the 'scores' slot in a 'ChIPScore' objectscores
~~ Methods for Function 'scores' ~~scores-methods
Searching function for Sites above threshold and predicted ChIP-seq ProfilessearchSites
setChromatinStatessetChromatinStates
~~ Methods for Function 'show' ~~show,ChIPScore-method show,genomicProfiles-method show,parameterOptions-method show-methods
singleRunsingleRun
Get Training and Testing data from ChIPscore objectssplitData
Accessor method of the 'stepSize' slot in 'parameterOptions' objectstepSize
~~ Methods for Function 'stepSize' ~~stepSize-methods
Setter Method for the 'stepSize' slot in a 'parameterOptions'stepSize<-
~~ Methods for Function 'stepSize<-' ~~stepSize<--methods
Accessor Method for the 'strandRule' slot in a 'parameterOptions' objectstrandRule
~~ Methods for Function 'strandRule' ~~strandRule-methods
Setter method for the 'strandRule' slot in a 'parameterOptions' object.strandRule<-
~~ Methods for Function 'strandRule<-' ~~strandRule<--methods
Accessor method for the 'whichstrand' slot in a 'parameterOptions' objectwhichstrand
~~ Methods for Function 'whichstrand' ~~whichstrand-methods
Setter method for the 'whichstrand' slot in a 'parameterOptions' objectwhichstrand<-
~~ Methods for Function 'whichstrand<-' ~~whichstrand<--methods