{ "_id": "6a13fda2acfb0bcc41d36e7b", "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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"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 slot of the BSFDataSet object", "topics": [ "setSummary", "setSummary,BSFDataSet-method" ] }, { "page": "show", "title": "Show method to for the BSFDataSet", "topics": [ "show", "show,BSFDataSet-method" ] }, { "page": "subset-BSFDataSet", "title": "Subset a BSFDataSet object", "topics": [ "subset-BSFDataSet", "[,BSFDataSet,ANY,ANY,ANY-method" ] }, { "page": "summary", "title": "Summary method to for the BSFDataSet", "topics": [ "summary", "summary,BSFDataSet-method" ] }, { "page": "supportRatio", "title": "Support ratio function for BSFDataSet objects", "topics": [ "supportRatio" ] }, { "page": "supportRatioPlot", "title": "Plot that shows the binding site support ratio", "topics": [ "supportRatioPlot" ] }, { "page": "targetGeneSpectrumPlot", "title": "Bar-chart to show the hosting gene types of binding sites", "topics": [ "targetGeneSpectrumPlot" ] }, { "page": "transcriptRegionOverlapsPlot", "title": "UpSet-plot to that shows the transcript region overlaps", "topics": [ "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", 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{ "source": "vignette.Rmd", "filename": "vignette.html", "title": "Definition of binding sites from iCLIP signal", "author": "Mirko Brüggemann, Kathi Zarnack", "engine": "knitr::rmarkdown", "headings": [ "Preface", "Motivation", "Prerequisites", "Installation", "Quick start", "A quick look at the input data", "A quick way to define binding sites", "The quick picture, two figures for the lazy one", "Standard workflow", "Manage the input data", "Build the BSFDataSet", "Construct the annotation objects", "Create annotation for genes", "Create annotation for transcript regions", "Performing the main analysis", "Deciding on the binding site width", "Pre-filtering of crosslink sites", "Selection of the binding site width", "Apply the gene-wise filter", "Merge crosslink sites into binding sites", "How to ensure reproducibility among replicates", "The replicate-specific threshold", "How many replicates are enough?", "Do my replicate corrlate well?", "Genomic target identification", "Target gene identification", "Transcript region identification", "Assessing further binding site properties", "Binding site strength", "Binding site definedness", "Exporting your results", "For additional analysis in R/Bioconductor", "Export as UCSC BED", "Export genes and feature lists", "Export iCLIP signal", "Diagnostic coverage polots", "Visualize the iCLIP coverage", "Trace back a binding site", "Gene wise coverage", "Variations of the standard workflow", "Normalize transcript regions", "How to manually test different binding site sizes", "If you already know your binding site size", "Call utility functions seperately", "Construct your own pipeline", "Work without a gene annotation", "Reproducibility scatter before and after correction", "Use a different set of transcript regions", "Additional functions", "Subset data for faster iterations", "Merge replicate signal", "Exporting iCLIP signal", "Calculate coverage", "Differential binding analysis", "Concept and idea", "Preparation of the input data", "Define binding sites for each condition", "Merge binding sites into a single object for testing", "Count matrix generation", "Calculate binding sites and background counts", "Filter binding site and background counts", "Perform differential testing", "Display differential results on gene level", "Differential binding variations", "Starting from scratch", "Starting from existing binding sites", "How to deal with multiple comparisons?", "Using the blacklist regions", "Session info", "Bibliography" ], "created": "2021-04-07 09:37:42", "modified": "2025-03-19 19:37:49", "commits": 26 } ], "_score": 5.431363764158988, "_indexed": true, "_nocasepkg": "bindingsitefinder", "_universes": [ "bioc", "mirkobr", "zarnackgroup" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.11.0", "date": "2026-05-25T06:50:46.000Z", "distro": "noble", "commit": "aec001f676114d29c45d7ffb6599cd6f075973a6", "fileid": "d9658e9cd3d5d9fc27a0bd00bff30895c1fcf9f64bf3825da617db1995b0a7ed", 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