{ "_id": "6a4949c2a788432aeabf4ace", "Package": "BindingSiteFinder", "Type": "Package", "Title": "Binding site defintion based on iCLIP data", "Version": "2.11.0", "Authors@R": "c(\nperson(\"Mirko\", \"Brüggemann\",\nemail=\"mirko.brueggemann@mail.de\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1778-0248\")),\nperson(\"Melina\", \"Klostermann\",\nemail=\"melinaklostermann@googlemail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-3122-1095\")),\nperson(\"Kathi\", \"Zarnack\",\nemail=\"kathi.zarnack@bmls.de\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-3527-3378\")))", "Description": "Precise knowledge on the binding sites of an RNA-binding\nprotein (RBP) is key to understand (post-) transcriptional\nregulatory processes. Here we present a workflow that describes\nhow exact binding sites can be defined from iCLIP data. The\npackage provides functions for binding site definition and\nresult visualization. For details please see the vignette.", "License": "Artistic-2.0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Collate": "'AllClasses.R' 'AllGenerics.R' 'Functions.R' 'methods.R'\n'bindingsites.R' 'helper.R' 'PlotFunction.R'\n'CoverageFunctions.R' 'workflow.R' 'helperSpecific.R'\n'exports.R' 'coveragePlots.R' 'bsfind.R' 'helperPlots.R'\n'differentialFunctions.R' 'differentialPlots.R'", "biocViews": "Sequencing, GeneExpression, GeneRegulation,\nFunctionalGenomics, Coverage, DataImport", "BugReports": "https://github.com/ZarnackGroup/BindingSiteFinder/issues", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:33 UTC", "RemoteUrl": "https://github.com/bioc/BindingSiteFinder", "RemoteRef": "HEAD", "RemoteSha": 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"author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380993 }, "_maintainer": { "name": "Mirko Brüggemann", "email": "mirko.brueggemann@mail.de", "login": "mirkobr", "twitter": "@MirkoBrBr", "description": "Bioinformatic researcher working in the field of (post-) transcriptional RNA regulation.", "uuid": 49233409, "orcid": "0000-0002-1778-0248" }, "_distro": "resolute", "_jobs": [ { "job": 85154255610, "time": 276, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8069618882" }, { "job": 85154255524, "time": 517, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8069698237" }, { "job": 85154255635, "time": 449, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8069676210" }, { "job": 85154255563, "time": 372, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8069650558" }, { "job": 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"processingStepsFlowChart", "processingStepsTable", "pureClipGeneWiseFilter", "pureClipGlobalFilter", "pureClipGlobalFilterPlot", "quickFigure", "rangeCoveragePlot", "reproducibilityCutoffPlot", "reproducibilityFilter", "reproducibilityFilterPlot", "reproducibilitySamplesPlot", "reproducibilityScatterPlot", "setMeta", "setName", "setRanges", "setSignal", "setSummary", "show", "summary", "supportRatio", "supportRatioPlot", "targetGeneSpectrumPlot", "transcriptRegionOverlapsPlot", "transcriptRegionSpectrumPlot" ], "_help": [ { "page": "add-BSFDataSet", "title": "Add two 'BSFDataSet' objects", "topics": [ "+,BSFDataSet,BSFDataSet-method", "add-BSFDataSet" ] }, { "page": "annotateWithScore", "title": "Annotation function for BSFDataSet object", "topics": [ "annotateWithScore" ] }, { "page": "assignToGenes", "title": "Assign binding sites to their hosting genes", "topics": [ "assignToGenes" ] }, { "page": "assignToTranscriptRegions", "title": "Assign binding sites to their hosting transcript regions", "topics": [ "assignToTranscriptRegions" ] }, { "page": "bindingSiteCoveragePlot", "title": "Plot signal coverage of selected ranges", "topics": [ "bindingSiteCoveragePlot" ] }, { "page": "bindingSiteDefinednessPlot", "title": "Binding site definedness plot", "topics": [ "bindingSiteDefinednessPlot" ] }, { "page": "BSFDataSet", "title": "BSFDataSet object and constructors", "topics": [ "BSFDataSet", "BSFDataSet,", "BSFDataSet-class,", "BSFDataSetFromBigWig" ] }, { "page": "BSFind", "title": "RBP binding site definition for iCLIP data", "topics": [ "BSFind" ] }, { "page": "calculateBsBackground", "title": "Compute background coverage for binding sites per gene", "topics": [ "calculateBsBackground" ] }, { "page": "calculateBsFoldChange", "title": "Compute fold-changes per binding site", "topics": [ "calculateBsFoldChange" ] }, { "page": "calculateSignalToFlankScore", "title": "Calculate signal-to-flank score", "topics": [ "calculateSignalToFlankScore" ] }, { "page": "clipCoverage", "title": "Coverage function for BSFDataSet objects", "topics": [ "clipCoverage" ] }, { "page": "collapseReplicates", "title": "Collapse signal from replicates", "topics": [ "collapseReplicates" ] }, { "page": "combineBSF", "title": "Combine multiple 'BSFDataSet' objects", "topics": [ "combineBSF" ] }, { "page": "coverageOverRanges", "title": "Coverage function for BSFDataSet objects", "topics": [ "coverageOverRanges" ] }, { "page": "duplicatedSitesPlot", "title": "Plot the number of overlaps when assigning crosslink sites to genes", "topics": [ "duplicatedSitesPlot" ] }, { "page": "estimateBsWidth", "title": "Function to estimate the appropriate binding site width together with the optimal gene-wise filter level.", "topics": [ "estimateBsWidth" ] }, { "page": "estimateBsWidthPlot", "title": "Plot the signal-to-flank score for varying gene-wise filter and binding site width", "topics": [ "estimateBsWidthPlot" ] }, { "page": "exportTargetGenes", "title": "Function to export sorted RBP target genes", "topics": [ "exportTargetGenes" ] }, { "page": "exportToBED", "title": "Wrapper function to export binding sites as BED files", "topics": [ "exportToBED" ] }, { "page": "filterBsBackground", "title": "Filter for genes not suitable for differential testing", "topics": [ "filterBsBackground" ] }, { "page": "geneOverlapsPlot", "title": "UpSet-plot to that shows the gene type overlaps", "topics": [ "geneOverlapsPlot" ] }, { "page": "geneRegulationPlot", "title": "Gene Regulation Plot", "topics": [ "geneRegulationPlot" ] }, { "page": "getMeta", "title": "Accessor method for the meta data of the BSFDataSet object", "topics": [ "getMeta", "getMeta,BSFDataSet-method" ] }, { "page": "getName", "title": "Accessor method for the name of the BSFDataSet object", "topics": [ "getName", "getName,BSFDataSet-method" ] }, { "page": "getRanges", "title": "Accessor method for the ranges of the BSFDataSet object", "topics": [ "getRanges", "getRanges,BSFDataSet-method" ] }, { "page": "getSignal", "title": "Accessor method for the signal data of the BSFDataSet object", "topics": [ "getSignal", "getSignal,BSFDataSet-method" ] }, { "page": "getSummary", "title": "Accessor method for the summary slot of the BSFDataSet object", "topics": [ "getSummary", "getSummary,BSFDataSet-method" ] }, { "page": "globalScorePlot", "title": "Plot the PureCLIP score distribution after re-assignment", "topics": [ "globalScorePlot" ] }, { "page": "imputeBsDifferencesForTestdata", "title": "Impute artificial differences in the example data set", "topics": [ "imputeBsDifferencesForTestdata" ] }, { "page": "makeBindingSites", "title": "Define equally sized binding sites from peak calling results and iCLIP crosslink events.", "topics": [ "makeBindingSites" ] }, { "page": "makeBsSummaryPlot", "title": "Plot binding site filter diagnostics", "topics": [ "makeBsSummaryPlot" ] }, { "page": "mergeCrosslinkDiagnosticsPlot", "title": "Plot binding site merging diagnostics", "topics": [ "mergeCrosslinkDiagnosticsPlot" ] }, { "page": "mergeSummaryPlot", "title": "Plot summarized results of the different binding site merging and filtering steps", "topics": [ "mergeSummaryPlot" ] }, { "page": "plotBsBackgroundFilter", "title": "Diagnostic plots for the differential binding background", "topics": [ "plotBsBackgroundFilter" ] }, { "page": "plotBsMA", "title": "MA style plot", "topics": [ "plotBsMA" ] }, { "page": "plotBsVolcano", "title": "Volcano style plot", "topics": [ "plotBsVolcano" ] }, { "page": "processingStepsFlowChart", "title": "Step-wise flowchart plot", "topics": [ "processingStepsFlowChart" ] }, { "page": "processingStepsTable", "title": "Create a table of all workflow steps for reporting", "topics": [ "processingStepsTable" ] }, { "page": "pureClipGeneWiseFilter", "title": "Filter PureCLIP sites by their score distribution per gene", "topics": [ "pureClipGeneWiseFilter" ] }, { "page": "pureClipGlobalFilter", "title": "Filter PureCLIP sites by their score distribution", "topics": [ "pureClipGlobalFilter" ] }, { "page": "pureClipGlobalFilterPlot", "title": "Plot the PureCLIP score distribution with global cutoff indicator", "topics": [ "pureClipGlobalFilterPlot" ] }, { "page": "quickFigure", "title": "Quick figures", "topics": [ "quickFigure" ] }, { "page": "rangeCoveragePlot", "title": "Plot crosslink event coverage over binding site range", "topics": [ "rangeCoveragePlot" ] }, { "page": "reproducibilityCutoffPlot", "title": "Plot to that shows how many replicates support each binding site", "topics": [ "reproducibilityCutoffPlot" ] }, { "page": "reproducibilityFilter", "title": "Replicate reproducibility filter function", "topics": [ "reproducibilityFilter" ] }, { "page": "reproducibilityFilterPlot", "title": "Plot to that shows the crosslink site distribution per replicate", "topics": [ "reproducibilityFilterPlot" ] }, { "page": "reproducibilitySamplesPlot", "title": "UpSet-plot to that shows how each replicate supports binding sites", "topics": [ "reproducibilitySamplesPlot" ] }, { "page": "reproducibilityScatterPlot", "title": "Plot that shows binding site reproducibility as scatter", "topics": [ "reproducibilityScatterPlot" ] }, { "page": "setMeta", "title": "Setter method for the meta data of the BSFDataSet object", "topics": [ "setMeta", "setMeta,BSFDataSet-method" ] }, { "page": "setName", "title": "Setter method for the names of the BSFDataSet object The name slot holds the name information of the dataset", "topics": [ "setName", "setName,BSFDataSet-method" ] }, { "page": "setRanges", "title": "Setter method for the ranges of the BSFDataSet object The GRanges object that holds the genomic ranges information can be replaced.", "topics": [ "setRanges", "setRanges,BSFDataSet-method" ] }, { "page": "setSignal", "title": "Setter method for the signal data of the BSFDataSet object", "topics": [ "setSignal", "setSignal,BSFDataSet-method" ] }, { "page": "setSummary", "title": "Setter method for the summary 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"transcriptRegionOverlapsPlot" ] }, { "page": "transcriptRegionSpectrumPlot", "title": "Bar-chart to show the hosting transcript regions of binding sites", "topics": [ "transcriptRegionSpectrumPlot" ] } ], "_readme": "https://github.com/bioc/BindingSiteFinder/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "cigarillo", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "digest", "distributional", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GetoptLong", "ggdist", "ggforce", "ggplot2", "GlobalOptions", "glue", "gtable", "highr", "htmltools", 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