{ "_id": "6a1fe387b401979e7343aa77", "Package": "CAGEfightR", "Type": "Package", "Title": "Analysis of Cap Analysis of Gene Expression (CAGE) data using\nBioconductor", "Version": "1.33.0", "Author": "Malte Thodberg", "Maintainer": "Malte Thodberg ", "Description": "CAGE is a widely used high throughput assay for measuring\ntranscription start site (TSS) activity. CAGEfightR is an\nR/Bioconductor package for performing a wide range of common\ndata analysis tasks for CAGE and 5'-end data in general. Core\nfunctionality includes: import of CAGE TSSs (CTSSs), tag (or\nunidirectional) clustering for TSS identification,\nbidirectional clustering for enhancer identification,\nannotation with transcript and gene models, correlation of TSS\nand enhancer expression, calculation of TSS shapes,\nquantification of CAGE expression as expression matrices and\ngenome brower visualization.", "URL": "https://github.com/MalteThodberg/CAGEfightR", "BugReports": "https://github.com/MalteThodberg/CAGEfightR/issues", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "biocViews": "Software, Transcription, Coverage, GeneExpression,\nGeneRegulation, PeakDetection, DataImport, DataRepresentation,\nTranscriptomics, Sequencing, Annotation, GenomeBrowsers,\nNormalization, Preprocessing, Visualization", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:47:57 UTC", "RemoteUrl": "https://github.com/bioc/CAGEfightR", "RemoteRef": "HEAD", "RemoteSha": "e0241fa3c36fb670d737488daadd2350af6cd36b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 08:08:07 UTC", "User": "root" }, "MD5sum": "2d17ad2012f0165120226fd637da456d", "_user": "bioc", "_type": "src", "_file": "CAGEfightR_1.33.0.tar.gz", "_fileid": "5be84ff9a1f457deeeb64794b795f378b734d5130fb195a2b2dac364059e242e", "_filesize": 1843814, "_sha256": "5be84ff9a1f457deeeb64794b795f378b734d5130fb195a2b2dac364059e242e", "_created": "2026-06-03T08:08:07.000Z", "_published": "2026-06-03T08:19:19.598Z", "_jobs": [ { "job": 79249823748, "time": 283, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7379167248" }, { "job": 79249823930, "time": 512, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7379242747" }, { "job": 79249823731, "time": 576, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7379264864" }, { "job": 79249823725, "time": 278, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7379165352" }, { "job": 79249823686, "time": 356, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7379189999" }, { "job": 79248566679, "time": 474, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7379067804" }, { "job": 79249823687, "time": 221, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7379146116" }, { "job": 79249823779, "time": 470, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7379228849" }, { "job": 79249823704, "time": 518, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7379246116" }, { "job": 79249823722, "time": 512, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7379242509" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CAGEfightR", "_commit": { "id": "e0241fa3c36fb670d737488daadd2350af6cd36b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380477 }, "_maintainer": { "name": "Malte Thodberg", "email": "maltethodberg@gmail.com", "login": "maltethodberg", "description": "", "uuid": 10612774 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.61.1", "role": "Depends" }, { "package": "rtracklayer", "version": ">= 1.69.1", "role": "Depends" }, { "package": "SummarizedExperiment", "version": ">= 1.39.1", "role": "Depends" }, { "package": "lobstr", "version": ">= 1.1.3", "role": "Imports" }, { "package": "purrr", "version": ">= 1.2.0", "role": "Imports" }, { "package": "assertthat", "version": ">= 0.2.0", "role": "Imports" }, { "package": "methods", "version": ">= 3.6.3", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.2-12", "role": "Imports" }, { "package": "BiocGenerics", "version": ">= 0.24.0", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.16.0", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.12.0", "role": "Imports" }, { "package": "Seqinfo", "version": ">= 1.0.0", "role": "Imports" }, { "package": "GenomicFeatures", "version": ">= 1.61.4", "role": "Imports" }, { "package": "GenomicAlignments", "version": ">= 1.45.1", "role": "Imports" }, { "package": "BiocParallel", "version": ">= 1.12.0", "role": "Imports" }, { "package": "GenomicFiles", "version": ">= 1.14.0", "role": "Imports" }, { "package": "Gviz", "version": ">= 1.22.2", "role": "Imports" }, { "package": "InteractionSet", "version": ">= 1.9.4", "role": "Imports" }, { "package": "GenomicInteractions", "version": ">= 1.15.1", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "org.Mm.eg.db", "role": "Suggests" }, { "package": "TxDb.Mmusculus.UCSC.mm9.knownGene", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-25", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-12", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.33.0", "bioc": "3.24" }, { "branch": "release", "version": "1.32.0", "bioc": "3.23" } ], "_topics": [ "software", "transcription", "coverage", "geneexpression", "generegulation", "peakdetection", "dataimport", "datarepresentation", "transcriptomics", "sequencing", "annotation", "genomebrowsers", "normalization", "preprocessing", "visualization" ], "_stars": 10, "_contributors": [ { "user": "maltethodberg", "count": 128, "uuid": 10612774 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 593, "source": "https://www.bioconductor.org/packages/stats/bioc/CAGEfightR" }, "_mentions": 6, "_devurl": "https://github.com/maltethodberg/cagefightr", "_searchresults": 126, "_rbuild": "4.6.0", "_assets": [ "extra/CAGEfightR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/maltethodberg/cagefightr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "assignGeneID", "assignMissingID", "assignTxID", "assignTxType", "balanceBC", "balanceD", "bwCommonGenome", "bwGenomeCompatibility", "bwValid", "calcBidirectionality", "calcComposition", "calcPooled", "calcShape", "calcSupport", "calcTotalTags", "calcTPM", "checkCTSSs", "checkPeaked", "checkPooled", "clusterBidirectionally", "clusterUnidirectionally", "combineClusters", "convertBAM2BigWig", "convertBED2BedGraph", "convertBED2BigWig", "convertBedGraph2BED", "convertBedGraph2BigWig", "convertBigWig2BED", "convertBigWig2BedGraph", "convertGRanges2GPos", "findLinks", "findStretches", "quantifyClusters", "quantifyCTSSs", "quantifyGenes", "quickEnhancers", "quickGenes", "quickTSSs", "shapeEntropy", "shapeIQR", "shapeMean", "subsetByBidirectionality", "subsetByComposition", "subsetBySupport", "swapRanges", "swapScores", "trackBalance", "trackClusters", "trackCTSS", "trackLinks", "trimToPeak", "trimToPercentiles", "tuneTagClustering", "utilsAggregateRows", "utilsDeStrand", "utilsScoreOverlaps", "utilsSimplifyTxDb" ], "_datasets": [ { "name": "exampleBidirectional", "title": "Example CAGE Data", "object": "exampleBidirectional", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "exampleCTSSs", "title": "Example CAGE Data", "object": "exampleCTSSs", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "exampleDesign", "title": "Example CAGE Data", "object": "exampleDesign", "class": [ "DFrame" ], "fields": [], "table": false, "tojson": false }, { "name": "exampleGenes", "title": "Example CAGE Data", "object": "exampleGenes", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "exampleUnidirectional", "title": "Example CAGE Data", "object": "exampleUnidirectional", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "assignGeneID", "title": "Annotate ranges with gene ID.", "concept": [ "Annotation functions" ], "topics": [ "assignGeneID", "assignGeneID,GenomicRanges,GenomicRanges-method", "assignGeneID,GenomicRanges,TxDb-method", "assignGeneID,RangedSummarizedExperiment,GenomicRanges-method", "assignGeneID,RangedSummarizedExperiment,TxDb-method" ] }, { "page": "assignMissingID", "title": "Annotate ranges with missing IDs.", "concept": [ "Annotation functions" ], "topics": [ "assignMissingID", "assignMissingID,character-method", "assignMissingID,GenomicRanges-method", "assignMissingID,RangedSummarizedExperiment-method" ] }, { "page": "assignTxID", "title": "Annotate ranges with transcript ID.", "concept": [ "Annotation functions" ], "topics": [ "assignTxID", "assignTxID,GenomicRanges,GenomicRanges-method", "assignTxID,GenomicRanges,TxDb-method", "assignTxID,RangedSummarizedExperiment,GenomicRanges-method", "assignTxID,RangedSummarizedExperiment,TxDb-method" ] }, { "page": "assignTxType", "title": "Annotate ranges with transcript type.", "concept": [ "Annotation functions" ], "topics": [ "assignTxType", "assignTxType,GenomicRanges,GenomicRangesList-method", "assignTxType,GenomicRanges,TxDb-method", "assignTxType,RangedSummarizedExperiment,GenomicRangesList-method", "assignTxType,RangedSummarizedExperiment,TxDb-method" ] }, { "page": "balanceBC", "title": "Balance statistic: Bhattacharyya coefficient (BC)", "topics": [ "balanceBC" ] }, { "page": "balanceD", "title": "Balance statistic: Andersson's D.", "topics": [ "balanceD" ] }, { "page": "bwCommonGenome", "title": "Find a common genome for a series of BigWig files.", "concept": [ "BigWig functions" ], "topics": [ "bwCommonGenome" ] }, { "page": "bwGenomeCompatibility", "title": "Check if BigWig-files are compatible with a given genome.", "concept": [ "BigWig functions" ], "topics": [ "bwGenomeCompatibility" ] }, { "page": "bwValid", "title": "Check if BigWig-files are valid.", "concept": [ "BigWig functions" ], "topics": [ "bwValid", "bwValid,BigWigFile-method", "bwValid,BigWigFileList-method" ] }, { "page": "calcBidirectionality", "title": "Calculate sample-wise bidirectionally of clusters.", "concept": [ "Calculation functions" ], "topics": [ "calcBidirectionality", "calcBidirectionality,GPos-method", "calcBidirectionality,GRanges-method", "calcBidirectionality,RangedSummarizedExperiment-method" ] }, { "page": "calcComposition", "title": "Calculate composition of CAGE data.", "concept": [ "Calculation functions" ], "topics": [ "calcComposition" ] }, { "page": "calcPooled", "title": "Calculate pooled expression across all samples.", "concept": [ "Calculation functions" ], "topics": [ "calcPooled" ] }, { "page": "calcShape", "title": "Calculate Tag Cluster shapes", "concept": [ "Calculation functions", "Shape functions" ], "topics": [ "calcShape", "calcShape,GRanges,GPos-method", "calcShape,GRanges,GRanges-method", "calcShape,GRanges,RangedSummarizedExperiment-method", "calcShape,RangedSummarizedExperiment,GRanges-method", "calcShape,RangedSummarizedExperiment,RangedSummarizedExperiment-method" ] }, { "page": "calcSupport", "title": "Calculate support of CAGE data.", "concept": [ "Calculation functions" ], "topics": [ "calcSupport" ] }, { "page": "calcTotalTags", "title": "Calculate the total number of CAGE tags across samples.", "concept": [ "Calculation functions" ], "topics": [ "calcTotalTags" ] }, { "page": "calcTPM", "title": "Calculate CAGE Tags-Per-Million (TPM)", "concept": [ "Calculation functions" ], "topics": [ "calcTPM" ] }, { "page": "checkCTSSs", "title": "Helper for checking files containing CTSSs", "topics": [ "checkCTSSs", "checkCTSSs,ANY-method", "checkCTSSs,BigWigFile-method", "checkCTSSs,character-method", "checkCTSSs,GPos-method", "checkCTSSs,GRanges-method" ] }, { "page": "checkPeaked", "title": "Helper for checking cluster with peaks", "concept": [ "Checking functions" ], "topics": [ "checkPeaked" ] }, { "page": "checkPooled", "title": "Helper for checking pooled signal", "concept": [ "Checking functions" ], "topics": [ "checkPooled" ] }, { "page": "clusterBidirectionally", "title": "Bidirectional clustering of pooled CTSSs.", "concept": [ "Clustering functions" ], "topics": [ "clusterBidirectionally", "clusterBidirectionally,GPos-method", "clusterBidirectionally,GRanges-method", "clusterBidirectionally,RangedSummarizedExperiment-method" ] }, { "page": "clusterUnidirectionally", "title": "Unidirectional Clustering (Tag Clustering) of pooled CTSSs.", "concept": [ "Clustering functions" ], "topics": [ "clusterUnidirectionally", "clusterUnidirectionally,GPos-method", "clusterUnidirectionally,GRanges-method", "clusterUnidirectionally,RangedSummarizedExperiment-method" ] }, { "page": "combineClusters", "title": "Combine two CAGE experiments.", "topics": [ "combineClusters", "combineClusters,RangedSummarizedExperiment,RangedSummarizedExperiment-method" ] }, { "page": "convertBAM2BigWig", "title": "Extract CTSSs from BAM-files (EXPERIMENTAL)", "topics": [ "convertBAM2BigWig" ] }, { "page": "convertBED2BigWig", "title": "Convert CTSSs stored in different file formats.", "topics": [ "convertBED2BedGraph", "convertBED2BigWig", "convertBedGraph2BED", "convertBedGraph2BigWig", "convertBigWig2BED", "convertBigWig2BedGraph" ] }, { "page": "convertGRanges2GPos", "title": "Convert GRanges with scores to GPos", "topics": [ "convertGRanges2GPos" ] }, { "page": "exampleDesign", "title": "Example CAGE Data", "topics": [ "exampleBidirectional", "exampleCTSSs", "exampleDesign", "exampleGenes", "exampleUnidirectional" ] }, { "page": "findLinks", "title": "Find nearby pairs of clusters and calculate pairwise correlations.", "concept": [ "Spatial functions" ], "topics": [ "findLinks", "findLinks,GRanges-method", "findLinks,RangedSummarizedExperiment-method" ] }, { "page": "findStretches", "title": "Find stretches of clusters", "concept": [ "Spatial functions" ], "topics": [ "findStretches", "findStretches,GRanges-method", "findStretches,RangedSummarizedExperiment-method" ] }, { "page": "quantifyClusters", "title": "Quantify expression of clusters (TSSs or enhancers) by summing CTSSs within clusters.", "concept": [ "Quantification functions" ], "topics": [ "quantifyClusters" ] }, { "page": "quantifyCTSSs", "title": "Quantify CAGE Transcriptions Start Sites (CTSSs)", "concept": [ "Quantification functions" ], "topics": [ "quantifyCTSSs", "quantifyCTSSs,BigWigFileList,BigWigFileList-method", "quantifyCTSSs,character,character-method" ] }, { "page": "quantifyCTSSs2", "title": "Quantify CAGE Transcriptions Start Sites (CTSSs)", "concept": [ "Quantification functions" ], "topics": [ "quantifyCTSSs2" ] }, { "page": "quantifyGenes", "title": "Quantify expression of genes", "concept": [ "Quantification functions" ], "topics": [ "quantifyGenes" ] }, { "page": "quickEnhancers", "title": "Identify and quantify enhancers.", "concept": [ "Wrapper functions" ], "topics": [ "quickEnhancers" ] }, { "page": "quickGenes", "title": "Identify and quantify genes.", "concept": [ "Wrapper functions" ], "topics": [ "quickGenes" ] }, { "page": "quickTSSs", "title": "Identify and quantify Transcription Start Sites (TSSs).", "concept": [ "Wrapper functions" ], "topics": [ "quickTSSs" ] }, { "page": "shapeEntropy", "title": "Shape statistic: Shannon Entropy", "concept": [ "Shape functions" ], "topics": [ "shapeEntropy" ] }, { "page": "shapeIQR", "title": "Shape statitic: Interquartile range", "concept": [ "Shape functions" ], "topics": [ "shapeIQR" ] }, { "page": "shapeMean", "title": "Shape statistic: Mean", "concept": [ "Shape functions" ], "topics": [ "shapeMean" ] }, { "page": "shapeMultimodality", "title": "Shape statistic: Multimodality", "topics": [ "shapeMultimodality" ] }, { "page": "subsetByBidirectionality", "title": "Subset by sample-wise bidirectionality of clusters.", "concept": [ "Calculation functions", "Subsetting functions" ], "topics": [ "subsetByBidirectionality", "subsetByBidirectionality,GPos-method", "subsetByBidirectionality,GRanges-method", "subsetByBidirectionality,RangedSummarizedExperiment-method" ] }, { "page": "subsetByComposition", "title": "Subset by composition across samples", "concept": [ "Calculation functions", "Subsetting functions" ], "topics": [ "subsetByComposition" ] }, { "page": "subsetBySupport", "title": "Subset by support across samples", "concept": [ "Calculation functions", "Subsetting functions" ], "topics": [ "subsetBySupport" ] }, { "page": "swapRanges", "title": "Swap ranges in a GRanges.", "concept": [ "Swapping functions" ], "topics": [ "swapRanges", "swapRanges,GenomicRanges-method", "swapRanges,RangedSummarizedExperiment-method" ] }, { "page": "swapScores", "title": "Swap scores in SummarizedExperiment", "concept": [ "Swapping functions" ], "topics": [ "swapScores" ] }, { "page": "trackBalance", "title": "Create Genome Browser Track of bidirectional balance scores", "concept": [ "Genome Browser functions" ], "topics": [ "trackBalance", "trackBalance,GPos-method", "trackBalance,GRanges-method", "trackBalance,RangedSummarizedExperiment-method" ] }, { "page": "trackClusters", "title": "Create genome browser track of clusters.", "concept": [ "Genome Browser functions" ], "topics": [ "trackClusters", "trackClusters,GRanges-method", "trackClusters,RangedSummarizedExperiment-method" ] }, { "page": "trackCTSS", "title": "Create Genome Browser track of CTSSs.", "concept": [ "Genome Browser functions" ], "topics": [ "trackCTSS", "trackCTSS,GPos-method", "trackCTSS,GRanges-method", "trackCTSS,RangedSummarizedExperiment-method" ] }, { "page": "trackLinks", "title": "Create a genome browser track of links.", "concept": [ "Genome Browser functions", "Spatial functions" ], "topics": [ "trackLinks" ] }, { "page": "trimToPeak", "title": "Trim width of TCs by distance from TC peak", "concept": [ "Clustering functions", "Trimming functions" ], "topics": [ "trimToPeak", "trimToPeak,GRanges,GPos-method", "trimToPeak,GRanges,GRanges-method", "trimToPeak,GRanges,RangedSummarizedExperiment-method", "trimToPeak,RangedSummarizedExperiment,GenomicRanges-method", "trimToPeak,RangedSummarizedExperiment,RangedSummarizedExperiment-method" ] }, { "page": "trimToPercentiles", "title": "Trim width of TCs to expression percentiles", "concept": [ "Clustering functions", "Trimming functions" ], "topics": [ "trimToPercentiles", "trimToPercentiles,GRanges,GPos-method", "trimToPercentiles,GRanges,GRanges-method", "trimToPercentiles,GRanges,RangedSummarizedExperiment-method", "trimToPercentiles,RangedSummarizedExperiment,GenomicRanges-method", "trimToPercentiles,RangedSummarizedExperiment,RangedSummarizedExperiment-method" ] }, { "page": "tuneTagClustering", "title": "Determine the optimal pooled threshold for unidirectional tag clustering.", "concept": [ "Clustering functions" ], "topics": [ "tuneTagClustering", "tuneTagClustering,GPos-method", "tuneTagClustering,GRanges-method", "tuneTagClustering,RangedSummarizedExperiment-method" ] }, { "page": "utilsAggregateRows", "title": "Utility: Aggregate rows", "concept": [ "Utility functions" ], "topics": [ "utilsAggregateRows", "utilsAggregateRows,dgCMatrix-method", "utilsAggregateRows,matrix-method" ] }, { "page": "utilsDeStrand", "title": "Utility: Split Genomic Ranges by strand", "concept": [ "Utility functions" ], "topics": [ "utilsDeStrand" ] }, { "page": "utilsScoreOverlaps", "title": "Utility: Counting overlaps taking into account scores", "concept": [ "Utility functions" ], "topics": [ "utilsScoreOverlaps" ] }, { "page": "utilsSimplifyTxDb", "title": "Utility: Extract annotation hierachy from a TxDb.", "concept": [ "Utility functions" ], "topics": [ "utilsSimplifyTxDb" ] } ], "_readme": "https://github.com/bioc/CAGEfightR/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "assertthat", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "dichromat", "digest", "dplyr", "ensembldb", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicInteractions", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "Gviz", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "InteractionSet", "interp", "IRanges", "isoband", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "latticeExtra", "lazyeval", "lifecycle", "lobstr", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ProtGenerics", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "Introduction_to_CAGEfightR.Rmd", "filename": "Introduction_to_CAGEfightR.html", "title": "Introduction to CAGEfightR", "author": "Malte Thodberg", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Citation", "Getting help", "Quick start for the impatient", "Introduction and overview", "Introduction to CAGE data", "Central S4-classes", "Overview of functions", "Pipeability", "Detailed Introduction", "CAGE Transcription Start Site (CTSS) level analysis", "Calculating pooled CTSSs", "Calculating CTSS support to remove excess noise", "Unidirectional (tag) clustering: Finding Transcription Start Sites (TSSs)", "Bidirectional clustering: Finding Enhancers", "Cluster level analysis", "Quantifying expression at cluster level", "Removing weakly expressed clusters", "Annotation with transcript models", "Quantifying shape of Tag Clusters", "Spatial analysis of clusters", "Gene level analysis", "Annotation with gene models", "Quantify expression at gene-level", "Filtering clusters based on gene composition", "Plotting CAGE data in a genome browser", "Parallel execution", "Session Info" ], "created": "2018-01-17 15:59:12", "modified": "2020-04-10 15:59:24", "commits": 15 } ], "_score": 8.35564305022087, "_indexed": true, "_nocasepkg": "cagefightr", "_universes": [ "bioc", "maltethodberg" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.33.0", "date": "2026-06-03T08:13:02.000Z", "distro": "noble", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "0df23467bafe687950efdf5041ef37fd7943cf35a82c983d95924469497c9726", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" }, { "r": "4.6.0", "os": "linux", "version": "1.33.0", "date": "2026-06-03T08:13:41.000Z", "distro": "noble", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "75ac9b1ae39abf8bec454e70d4ab12c045e45067db6ef5ef95c4e4ff0be568db", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" }, { "r": "4.5.3", "os": "mac", "version": "1.33.0", "date": "2026-06-03T08:10:56.000Z", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "8555cc747dec514965951d12f4be218308b7217d0d0b0364fbfa3bd92fd92e19", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" }, { "r": "4.6.0", "os": "mac", "version": "1.33.0", "date": "2026-06-03T08:11:08.000Z", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "375cfad620c218fb3819e19886120e2a7d3bcb3ba37a0f4cfcfa0421551e6d20", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" }, { "r": "4.6.0", "os": "wasm", "version": "1.33.0", "date": "2026-06-03T08:12:55.000Z", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "a476526287f7ff69aa2ddbf028b3d4d4171a6d09a758d64a8c5502bd6384a7f7", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" }, { "r": "4.7.0", "os": "win", "version": "1.33.0", "date": "2026-06-03T08:11:28.000Z", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "cd626a5f5c60f373983d555920acf052a2262ae7a84daf196780c5703b713803", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" }, { "r": "4.5.3", "os": "win", "version": "1.33.0", "date": "2026-06-03T08:11:49.000Z", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "70c9140861faee7a5c7358cce59c8800680aaec943faded2a8371e1b98046183", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" }, { "r": "4.6.0", "os": "win", "version": "1.33.0", "date": "2026-06-03T08:12:05.000Z", "commit": "e0241fa3c36fb670d737488daadd2350af6cd36b", "fileid": "7becead9c49b0b7521aa18f6039f323dabd46f6229c87b19495019623bd82a05", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871729860" } ] }