Package: ChIPanalyser 1.35.0

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_1.35.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ChIPanalyser/json (API)

# Install 'ChIPanalyser' in R:
install.packages('ChIPanalyser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • Access - ChIPanalyserData
  • chip - ChIPanalyserData
  • cs - ChIPanalyserData
  • geneRef - ChIPanalyserData
  • top - ChIPanalyserData

On BioConductor:ChIPanalyser-1.35.0(bioc 3.24)ChIPanalyser-1.34.0(bioc 3.23)

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

softwarebiologicalquestionworkflowsteptranscriptionsequencingchiponchipcoveragealignmentchipseqsequencematchingdataimportpeakdetection

4.84 score 23 scripts 1 mentions 74 exports 61 dependencies

Last updated from:65cc919cf0. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR224
linux-devel-x86_64NOTE424
source / vignettesOK1057
linux-release-x86_64NOTE421
macos-release-arm64NOTE266
macos-oldrel-arm64NOTE311
windows-develNOTE378
windows-releaseNOTE356
windows-oldrelNOTE370
wasm-releaseOK196

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

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsBSgenomecaToolscigarillocodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesgplotsgtoolshttrIRangesjsonliteKernSmoothlambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRcppRcppRollRCurlrestfulrRhtslibrjsonROCRRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryaml

The ChIPanalyser User's Guide
Introduction - What is this package? | Methods - The Model | Work Flow | Loading Data | Quick Start | Step 1 - Extracting Normalised ChIP scores from ChIP-seq datasets | Step 2 - Computing a PWMs | Step 3 - Computing Optimal Parameters | Step 4 - Extracting Optimal Paramters (Prelim) | Step 5 - Plotting Optimal Set of Parameters | Step 6 - Extracting Optimal Set of Parameters with associated data | Step 7 - Plotting ChIP_seq like profiles | Advanced Work | Step 1 - Parameter Set Up | Step 2 - Extracting Normalised ChIP scores. | Step 3 - Position Weight Matrix and Associated Paramters | Step 4 - Computing Optimal Set of Parameters | Step 5 - Extracting and Plotting Optimal Parameters | Step 6 - Computing individual parameter combinations | Step 7 - Plotting Single combination | Parameter Description | Session Info | References
Rendered fromChIPanalyser.Rmdusingknitr::rmarkdown

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

The ChIPanalyser User's Guide
Introduction - What is this package? | Methods - The Chromatin State Model | Using ChIPanalyser | Loading data | ChIPanalyser | External Data | Input data : What is it? | Setting Parameters | Initializing ChIPanalyser | Building Initial objects | Generating a starting population | Pre-processing ChIP data | Evolution | Fitest of them all | Get fitest individual | Running ChIPanalyser with fitest individual | Plotting
Rendered fromGA_ChIPanalyser.Rmdusingknitr::rmarkdown

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