{ "_id": "6a19680facfb0bcc41de8487", "Package": "ChIPanalyser", "Type": "Package", "Title": "ChIPanalyser: Predicting Transcription Factor Binding Sites", "Authors@R": "c(\nperson(c(\"Patrick\", \"CN\"), \"Martin\", role=c(\"cre\", \"aut\"), email=\"pcnmartin@gmail.com\"),\nperson(c(\"Nicolea\",\"Radu\"), \"Zabet\", role=\"aut\"))", "Version": "1.35.0", "Date": "2017-09-01", "Author": "Patrick C.N.Martin & Nicolae Radu Zabet", "Maintainer": "Patrick C.N. Martin ", "Citation": "Zabet NR, Adryan B (2015) Estimating binding properties of\ntranscription factors from genome-wide binding profiles.\nNucleic Acids Res., 43, 84–94.", "Description": "ChIPanalyser is a package to predict and understand TF\nbinding by utilizing a statistical thermodynamic model. The\nmodel incorporates 4 main factors thought to drive TF binding:\nChromatin State, Binding energy, Number of bound molecules and\na scaling factor modulating TF binding affinity. Taken\ntogether, ChIPanalyser produces ChIP-like profiles that closely\nmimic the patterns seens in real ChIP-seq data.", "License": "GPL-3", "Collate": "2AllS4Class_ProfileParameters.R 3AllGenerics.R 4AllMethods.R\nAllInitialize.R AllShowMethods.R computeChIPProfile.R\ncomputeOccupancy.R computeOptimal.R computePWMScore.R\ncomputeGenomeWide.R parallelInternalFunctionsDev.R\nGenomicProfileGenericFunctions.R plotOccupancy.R\nplotOptimalHeatMapDev.R DataPreprocessingDev.R\nDataPreprocessingGenericFunctionsDev.R\nprofileAccuracyEstimateDev.R GAAnalysis.R GAGeneric.R", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "Software, BiologicalQuestion, WorkflowStep, Transcription,\nSequencing, ChipOnChip, Coverage, Alignment, ChIPSeq,\nSequenceMatching, DataImport ,PeakDetection", "VignetteBuilder": "knitr", "RoxygenNote": "7.2.1", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:20 UTC", "RemoteUrl": "https://github.com/bioc/ChIPanalyser", "RemoteRef": "HEAD", "RemoteSha": "65cc919cf0a80ac81ac3e0b7e99c1cd18e253f34", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:31:36 UTC", "User": "root" }, "MD5sum": "6c7f343267c29dcc7e87675fe97f5bb1", "_user": "bioc", "_type": "src", "_file": "ChIPanalyser_1.35.0.tar.gz", "_fileid": "ed092125431c073d801ddf8f84c8a354033fdee5486d7a85e216378b939543aa", "_filesize": 2808993, "_sha256": "ed092125431c073d801ddf8f84c8a354033fdee5486d7a85e216378b939543aa", "_created": "2026-05-29T08:31:36.000Z", "_published": "2026-05-29T10:18:55.058Z", "_jobs": [ { "job": 78466173156, "time": 238, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7286570148" }, { "job": 78466173120, "time": 434, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7286625926" }, { "job": 78466173127, "time": 439, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7286627246" }, { "job": 78466173129, "time": 355, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7288401420" }, { "job": 78466173168, "time": 214, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7288361149" }, { "job": 78463430270, "time": 1140, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286495885" }, { "job": 78466173143, "time": 169, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286549638" }, { "job": 78466173124, "time": 438, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7286627052" }, { "job": 78466173146, "time": 364, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7286606717" }, { "job": 78466173181, "time": 397, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7286615751" } ], "_bioccheck": { "error": 2, "warning": 4, "note": 20 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626185666", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ChIPanalyser", "_commit": { "id": "65cc919cf0a80ac81ac3e0b7e99c1cd18e253f34", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380380 }, "_maintainer": { "name": "Patrick C.N. 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Methods for Function 'chipSmooth' ~~", "topics": [ "chipSmooth-methods" ] }, { "page": "chipSmooth_-", "title": "Setter method for 'chipSmooth' slot in 'parameterOptions' object.", "topics": [ "chipSmooth<-" ] }, { "page": "chipSmooth_--methods", "title": "~~ Methods for Function 'chipSmooth<-' ~~", "topics": [ "chipSmooth<--methods" ] }, { "page": "computeChIPProfile", "title": "Computing ChIP-seq like profiles from Occupancy data.", "topics": [ "computeChIPProfile" ] }, { "page": "computeGenomeWideScores", "title": "Computing Genome Wide scores", "topics": [ "computeGenomeWideScores" ] }, { "page": "computeOccupancy", "title": "Compute Occupancy values from PWM Scores based on model.", "topics": [ "computeOccupancy" ] }, { "page": "computeOptimal", "title": "compute Optimal Parameters", "topics": [ "computeOptimal" ] }, { "page": "computePWMScore", "title": "Compute PWM Scores of sites above threshold.", "topics": [ "computePWMScore" ] }, { "page": "DNASequenceLength", "title": 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"genomicProfilesInternal-class", "title": "Class '\"genomicProfilesInternal\"'", "topics": [ ".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", 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"title": "~~ Methods for Function 'initialize' ~~", "topics": [ "initialize,ChIPScore-method", "initialize,genomicProfiles-method", "initialize,parameterOptions-method", "initialize-methods" ] }, { "page": "lambdaPWM", "title": "Accessor Method for the 'lambdaPWM' slot in a 'parameterOptions' object", "topics": [ "lambdaPWM" ] }, { "page": "lambdaPWM-methods", "title": "~~ Methods for Function 'lambdaPWM' ~~", "topics": [ "lambdaPWM-methods" ] }, { "page": "lambdaPWM_", "title": "Setter Method for the 'lambdaPWM' slot in a 'parameterOptions' object", "topics": [ "lambdaPWM<-" ] }, { "page": "lambdaPWM_--methods", "title": "~~ Methods for Function 'lambdaPWM<-' ~~", "topics": [ "lambdaPWM<--methods" ] }, { "page": "loci", "title": "Accessor Method for the 'loci' slot in a 'ChIPScore' object", "topics": [ "loci" ] }, { "page": "loci-class", "title": "Class '\"loci\"'", "topics": [ "loci-class" ] }, { "page": "loci-methods", "title": "~~ Methods for Function 'loci' ~~", "topics": [ "loci-methods" ] }, { "page": "lociWidth", "title": "Accessor Method for the 'lociWidth' slot in a 'parameterOptions' object", "topics": [ "lociWidth" ] }, { "page": "lociWidth-methods", "title": "~~ Methods for Function 'lociWidth' ~~", "topics": [ "lociWidth-methods" ] }, { "page": "lociWidth_", "title": "Setter Method for the 'lociWidth' slot in a 'parameterOptions' object", "topics": [ "lociWidth<-" ] }, { "page": "lociWidth_--methods", "title": "~~ Methods for Function 'lociWidth<-' ~~", "topics": [ "lociWidth<--methods" ] }, { "page": "maxPWMScore", "title": "Accessor function for 'maxPWMScore' slot in a 'genomicProfiles' object.", "topics": [ "maxPWMScore" ] }, { "page": "maxPWMScore-methods", "title": "~~ Methods for Function 'maxPWMScore' ~~", "topics": [ "maxPWMScore-methods" ] }, { "page": "maxSignal", "title": "Accessor method for the 'maxSignal' slot in a 'parameterOptions' object.", "topics": [ "maxSignal" ] }, { "page": "maxSignal-methods", "title": "~~ Methods for Function 'maxSignal' ~~", "topics": [ "maxSignal-methods" ] }, { "page": "maxSignal_-", "title": "Setter method for 'maxSignal' slot in a 'parameterOptions' object.", "topics": [ "maxSignal<-" ] }, { "page": "maxSignal_--methods", "title": "~~ Methods for Function 'maxSignal<-' ~~", "topics": [ "maxSignal<--methods" ] }, { "page": "minPWMScore", "title": "Accessor method the 'minPWMScore' slot in a 'genomicProfiles' object", "topics": [ "minPWMScore" ] }, { "page": "minPWMScore-methods", "title": "~~ Methods for Function 'minPWMScore' ~~", "topics": [ "minPWMScore-methods" ] }, { "page": "naturalLog", "title": "Accessor method the 'naturalLog' slot in a 'parameterOptions' object.", "topics": [ "naturalLog" ] }, { "page": "naturalLog-methods", "title": "~~ Methods for Function 'naturalLog' ~~", "topics": [ "naturalLog-methods" ] }, { "page": "naturalLog_-", "title": "Setter method for the 'naturalLog' slot in a 'parameterOptions' object.", "topics": [ "naturalLog<-" ] }, { "page": 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'parameterOptions' object.", "topics": [ "noOfSites<-" ] }, { "page": "noOfSites_--methods", "title": "~~ Methods for Function 'noOfSites<-' ~~", "topics": [ "noOfSites<--methods" ] }, { "page": "nos-class", "title": "Class '\"nos\"'", "topics": [ "nos-class" ] }, { "page": "parameterOptions", "title": "parameter Options object", "topics": [ "parameterOptions" ] }, { "page": "parameterOptions-class", "title": "Class '\"parameterOptions\"'", "topics": [ ".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" ] }, { "page": "PFMFormat", "title": "Accesor method for the 'PFMFormat' slot in a 'genomicProfiles' object", "topics": [ "PFMFormat" ] }, { "page": "PFMFormat-methods", "title": "~~ Methods for Function 'PFMFormat' ~~", "topics": [ "PFMFormat-methods" ] }, { "page": "PFMFormat_", "title": "Setter method for the 'PFMFormat' slot in a 'genomicProfiles' object", "topics": [ "PFMFormat<-" ] }, { "page": "PFMFormat_--methods", "title": "~~ Methods for Function 'PFMFormat<-' ~~", "topics": [ "PFMFormat<--methods" ] }, { "page": "ploidy", "title": "Accessor method for the 'ploidy' slot in a 'parameterOptions' object", "topics": [ "ploidy" ] }, { "page": "ploidy-methods", "title": "~~ Methods for Function 'ploidy' ~~", "topics": [ "ploidy-methods" ] }, { "page": "ploidy_-", "title": "Setter Method for the 'ploidy' slot in an 'parameterOptions' object", "topics": [ "ploidy<-" ] }, { "page": "ploidy_--methods", "title": "~~ Methods for Function 'ploidy<-' ~~", "topics": [ "ploidy<--methods" ] }, { "page": "plotOccupancyProfile", "title": "Plot Occupancy Profiles", "topics": [ "plotOccupancyProfile" ] }, { "page": "plotOptimalHeatMaps", "title": "Heat Map of optimal Parameters", "topics": [ "plotOptimalHeatMaps" ] }, { "page": "PositionFrequencyMatrix", "title": "Accessor method for the 'PFM' slot in a 'genomicProfiles' object", "topics": [ "PositionFrequencyMatrix" ] }, { "page": "PositionFrequencyMatrix-methods", "title": "~~ Methods for Function 'PositionFrequencyMatrix' ~~", "topics": [ "PositionFrequencyMatrix-methods" ] }, { "page": "PositionFrequencyMatrix_-", "title": "Setter method for the 'PFM' slot in a 'genomicProfiles' object", "topics": [ "PositionFrequencyMatrix<-" ] }, { "page": "PositionFrequencyMatrix_--methods", "title": "~~ Methods for Function 'PositionFrequencyMatrix<-' ~~", "topics": [ "PositionFrequencyMatrix<--methods" ] }, { "page": "PositionWeightMatrix", "title": "Accessor Method for the 'PWM' slot in a 'genomicProfiles' object", "topics": [ "PositionWeightMatrix" ] }, { "page": "PositionWeightMatrix-methods", "title": "~~ Methods for Function 'PositionWeightMatrix' ~~", "topics": [ "PositionWeightMatrix-methods" ] }, { "page": "PositionWeightMatrix_-", "title": "Setter Method for the 'PositionWeightMatrix' slot in a 'genomicProfiles' object", "topics": [ "PositionWeightMatrix<-" ] }, { "page": "PositionWeightMatrix_--methods", "title": "~~ Methods for Function 'PositionWeightMatrix<-' ~~", "topics": [ "PositionWeightMatrix<--methods" ] }, { "page": "processingChIP", "title": "Pre-processing ChIP-seq data", "topics": [ "processingChIP" ] }, { "page": "profileAccuracyEstimate", "title": "Estimating Accuracy of predicted Profiles", "topics": [ "profileAccuracyEstimate" ] }, { "page": "profiles-methods", "title": "~~ Methods for Function 'profiles' ~~", "topics": [ "profiles" ] }, { "page": "PWMpseudocount", "title": "Accessor Method for a 'PWMpseudocount' slot in a 'parameterOptions'", "topics": [ "PWMpseudocount" ] }, { "page": "PWMpseudocount-methods", "title": "~~ Methods for Function 'PWMpseudocount' ~~", "topics": [ "PWMpseudocount-methods" ] }, { "page": "PWMpseudocount_-", "title": "Setter Method for the 'pseudocount' slot in a 'parameterOptions' object", "topics": [ "PWMpseudocount<-" ] }, { "page": "PWMpseudocount_--methods", "title": "~~ Methods for Function 'PWMpseudocount<-' ~~", "topics": [ "PWMpseudocount<--methods" ] }, { "page": "PWMThreshold", "title": "Accessor method for the 'PWMThreshold' slot in a 'parameterOptions' object", "topics": [ "PWMThreshold" ] }, { "page": "PWMThreshold-methods", "title": "~~ Methods for Function 'PWMThreshold' ~~", "topics": [ "PWMThreshold-methods" ] }, { "page": "PWMThreshold_-", "title": "Setter Method for the 'PWMThreshold' slot in a 'parameterOptions' object", "topics": [ "PWMThreshold<-" ] }, { "page": "PWMThreshold_--methods", "title": "~~ Methods for Function 'PWMThreshold<-' ~~", "topics": [ "PWMThreshold<--methods" ] }, { "page": "removeBackground", "title": "Accessor Method for the 'removeBackground' slot in a 'parameterOptions' object", "topics": [ "removeBackground" ] }, { "page": "removeBackground-methods", "title": "~~ Methods for Function 'removeBackground' ~~", "topics": [ "removeBackground-methods" ] }, { "page": "removeBackground_-", "title": "Setter Method for the 'removeBackground' slot in a 'parameterOptions' object", "topics": [ "removeBackground<-" ] }, { "page": "removeBackground_--methods", "title": "~~ Methods for Function 'removeBackground<-' ~~", "topics": [ "removeBackground<--methods" ] }, { "page": "scores", "title": "Accessor Method for the 'scores' slot in a 'ChIPScore' object", "topics": [ "scores" ] }, { "page": "scores-methods", "title": "~~ Methods for Function 'scores' ~~", "topics": [ "scores-methods" ] }, { "page": "searchSites", "title": "Searching function for Sites above threshold and predicted ChIP-seq Profiles", "topics": [ "searchSites" ] }, { "page": "setChromatinStates", "title": "setChromatinStates", "topics": [ "setChromatinStates" ] }, { "page": "show-methods", "title": "~~ Methods for Function 'show' ~~", "topics": [ "show,ChIPScore-method", "show,genomicProfiles-method", "show,parameterOptions-method", "show-methods" ] }, { "page": "singleRun", "title": "singleRun", "topics": [ "singleRun" ] }, { "page": "splitData", "title": "Get Training and Testing data from ChIPscore objects", "topics": [ "splitData" ] }, { "page": "stepSize", "title": "Accessor method of the 'stepSize' slot in 'parameterOptions' object", "topics": [ "stepSize" ] }, { "page": "stepSize-methods", "title": "~~ Methods for Function 'stepSize' ~~", "topics": [ "stepSize-methods" ] }, { "page": "stepSize_-", "title": "Setter Method for the 'stepSize' slot in a 'parameterOptions'", "topics": [ "stepSize<-" ] }, { "page": "stepSize_--methods", "title": "~~ Methods for Function 'stepSize<-' ~~", "topics": [ "stepSize<--methods" ] }, { "page": "strandRule", "title": "Accessor Method for the 'strandRule' slot in a 'parameterOptions' object", "topics": [ "strandRule" ] }, { "page": "strandRule-methods", "title": "~~ Methods for Function 'strandRule' ~~", "topics": [ "strandRule-methods" ] }, { "page": "strandRule_-", "title": "Setter method for the 'strandRule' slot in a 'parameterOptions' object.", "topics": [ "strandRule<-" ] }, { "page": "strandRule_--methods", "title": "~~ Methods for Function 'strandRule<-' ~~", "topics": [ "strandRule<--methods" ] }, { "page": "whichstrand", "title": "Accessor method for the 'whichstrand' slot in a 'parameterOptions' object", "topics": [ "whichstrand" ] }, { "page": "whichstrand-methods", "title": "~~ Methods for Function 'whichstrand' ~~", "topics": [ "whichstrand-methods" ] }, { "page": "whichstrand_-", "title": "Setter method for the 'whichstrand' slot in a 'parameterOptions' object", "topics": [ "whichstrand<-" ] }, { "page": "whichstrand_--methods", "title": "~~ Methods for Function 'whichstrand<-' ~~", "topics": [ "whichstrand<--methods" ] } ], "_readme": "https://github.com/bioc/ChIPanalyser/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "Biostrings", "bitops", "BSgenome", "caTools", "cigarillo", "codetools", "cpp11", "crayon", "curl", "DelayedArray", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "gplots", "gtools", "httr", "IRanges", "jsonlite", "KernSmooth", "lambda.r", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "R6", "RColorBrewer", "Rcpp", "RcppRoll", "RCurl", "restfulr", "Rhtslib", "rjson", "ROCR", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "UCSC.utils", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "ChIPanalyser.Rmd", "filename": "ChIPanalyser.html", "title": "The ChIPanalyser User's Guide", "author": "Patrick Martin", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2017-08-24 14:17:33", "modified": "2022-09-02 10:24:50", "commits": 15 }, { "source": "GA_ChIPanalyser.Rmd", "filename": "GA_ChIPanalyser.html", "title": "The ChIPanalyser User's Guide", "author": "Patrick Martin", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2022-09-02 10:24:50", 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