{ "_id": "6a19724aacfb0bcc41dee88f", "Package": "CAGEr", "Title": "Analysis of CAGE (Cap Analysis of Gene Expression) sequencing\ndata for precise mapping of transcription start sites and\npromoterome mining", "Version": "2.19.0", "Date": "2025-10-10", "Authors@R": "c( person(\"Vanja\", \"Haberle\", email = \"vanja.haberle@gmail.com\", role = \"aut\"),\nperson(\"Charles\", \"Plessy\", email = \"charles.plessy@oist.jp\", role = \"cre\"),\nperson(\"Damir\", \"Baranasic\", email = \"damir.baranasic@lms.mrc.ac.uk\", role = \"ctb\"),\nperson(\"Katalin\", \"Ferenc\", email = \"k.t.ferenc@ncmbm.uio.no\", role = \"ctb\"),\nperson(\"Sarvesh\", \"Nikumbh\", email = \"s.nikumbh@lms.mrc.ac.uk\", role = \"ctb\")\n)", "Description": "The _CAGEr_ package identifies transcription start sites\n(TSS) and their usage frequency from CAGE (Cap Analysis Gene\nExpression) sequencing data. It normalises raw CAGE tag count,\nclusters TSSs into tag clusters (TC) and aggregates them across\nmultiple CAGE experiments to construct consensus clusters (CC)\nrepresenting the promoterome. CAGEr provides functions to\nprofile expression levels of these clusters by cumulative\nexpression and rarefaction analysis, and outputs the plots in\nggplot2 format for further facetting and customisation. After\nclustering, CAGEr performs analyses of promoter width and\ndetects differential usage of TSSs (promoter shifting) between\nsamples. CAGEr also exports its data as genome browser tracks,\nand as R objects for downsteam expression analysis by other\nBioconductor packages such as DESeq2, CAGEfightR, or seqArchR.", "License": "GPL-3", "biocViews": "Preprocessing, Sequencing, Normalization,\nFunctionalGenomics, Transcription, GeneExpression, Clustering,\nVisualization", "Collate": "'Multicore.R' 'CTSS.R' 'CAGEexp.R' 'ClusteringFunctions.R'\n'ClusteringMethods.R' 'CAGEr.R' 'Annotations.R'\n'AggregationMethods.R' 'CAGEfightR.R' 'CAGEr-package.R'\n'Paraclu.R' 'CorrelationMethods.R' 'GetMethods.R'\n'CumulativeDistributionMethods.R' 'Distclu.R' 'ExportMethods.R'\n'ExpressionProfilingMethods.R' 'ImportFunctions.R'\n'SetMethods.R' 'ImportMethods.R' 'MergingMethods.R'\n'NormalizationFunctions.R' 'NormalizationMethods.R'\n'QCmethods.R' 'QuantileWidthMethods.R' 'ResetMethods.R'\n'Richness.R' 'RleDataFrame.R' 'ShiftingFunctions.R'\n'ShiftingMethods.R' 'StrandInvaders.R' 'TSSlogo.R'", "LazyData": "true", "VignetteBuilder": "knitr", 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"title": "Extracting library sizes from CAGEr objects", "concept": [ "CAGEr accessor methods" ], "topics": [ "librarySizes", "librarySizes,CAGEexp-method" ] }, { "page": "loadFileIntoGPos", "title": "loadFileIntoGPos", "concept": [ "loadFileIntoGPos" ], "topics": [ "loadFileIntoGPos" ] }, { "page": "mapStats", "title": "Process mapping statistics", "topics": [ "mapStats" ] }, { "page": "mapStatsScopes", "title": "mapStats scopes", "topics": [ "mapStatsScopes", "msScope_all", "msScope_annotation", "msScope_counts", "msScope_mapped", "msScope_qc", "msScope_steps" ] }, { "page": "mergeCAGEsets", "title": "Merge two CAGEr objects into one", "topics": [ "mergeCAGEsets", "mergeCAGEsets,CAGEexp,CAGEexp-method" ] }, { "page": "mergeSamples", "title": "Merge CAGE samples", "topics": [ "mergeSamples", "mergeSamples,CAGEexp-method" ] }, { "page": "moleculesGR2CTSS", "title": "moleculesGR2CTSS", "concept": [ "loadFileIntoGPos" ], "topics": [ "moleculesGR2CTSS" ] }, { "page": "normalizeTagCount", "title": "Normalizing raw CAGE tag count", "concept": [ "CAGEr normalised data functions", "CAGEr object modifiers" ], "topics": [ "normalizeTagCount", "normalizeTagCount,CAGEexp-method" ] }, { "page": "paraclu", "title": "Parametric clustering", "concept": [ "CAGEr clustering methods", "CAGEr clusters functions", "CAGEr object modifiers" ], "topics": [ "paraclu", "paraclu,CAGEexp-method", "paraclu,CTSS-method", "paraclu,GRanges-method", "paraclu,Pairs-method", "paraclu,SummarizedExperiment-method" ] }, { "page": "parseCAGEscanBlocksToGrangeTSS", "title": "parseCAGEscanBlocksToGrangeTSS", "topics": [ "parseCAGEscanBlocksToGrangeTSS" ] }, { "page": "plot.hanabi", "title": "Plotting Hanabi objects", "concept": [ "CAGEr richness functions" ], "topics": [ "lines.hanabi", "plot.hanabi", "points.hanabi" ] }, { "page": "plotAnnot", "title": "Plot annotation statistics", "concept": [ "CAGEr annotation functions", "CAGEr plot functions" ], "topics": [ "plotAnnot", "plotAnnot,CAGEexp-method", "plotAnnot,data.frame-method", "plotAnnot,DataFrame-method", "plotAnnot,GRangesList-method" ] }, { "page": "plotCorrelation", "title": "Pairwise scatter plots and correlations of CAGE signal", "concept": [ "CAGEr plot functions" ], "topics": [ "correlationMatrix", "correlationMatrix,CAGEexp-method", "correlationMatrix,data.frame-method", "correlationMatrix,DataFrame-method", "correlationMatrix,matrix-method", "correlationMatrix,SummarizedExperiment-method", "plotCorrelation", "plotCorrelation,CAGEr-method", "plotCorrelation2", "plotCorrelation2,CAGEexp-method", "plotCorrelation2,data.frame-method", "plotCorrelation2,DataFrame-method", "plotCorrelation2,matrix-method", "plotCorrelation2,SummarizedExperiment-method" ] }, { "page": "plotExpressionProfiles", "title": "Plot CAGE expression profiles", "concept": [ "CAGEr expression clustering functions", "CAGEr plot functions" ], "topics": [ "plotExpressionProfiles", "plotExpressionProfiles,CAGEexp-method" ] }, { "page": "plotInterquantileWidth", "title": "Plot cluster widths", "concept": [ "CAGEr clusters functions", "CAGEr plot functions" ], "topics": [ "plotInterquantileWidth", "plotInterquantileWidth,CAGEexp-method" ] }, { "page": "plotReverseCumulatives", "title": "Plot reverse cumulative number of CAGE tags per CTSS", "concept": [ "CAGEr normalised data functions", "CAGEr plot functions" ], "topics": [ "plotReverseCumulatives", "plotReverseCumulatives,CAGEexp-method", "plotReverseCumulatives,GRanges-method", "plotReverseCumulatives,GRangesList-method" ] }, { "page": "quantilePositions", "title": "Determine CTSS quantile positions within clusters", "concept": [ "CAGEr clusters functions", "CAGEr object modifiers" ], "topics": [ "quantilePositions", "quantilePositions,CAGEexp-method" ] }, { "page": "quickEnhancers", "title": "Identify and quantify enhancers.", "concept": [ "CAGEfightR", "CAGEr object modifiers" ], "topics": [ "quickEnhancers", "quickEnhancers,CAGEexp-method" ] }, { "page": 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