{
  "_id": "6a4de2d4d253724d3f6ddb7f",
  "Package": "Damsel",
  "Type": "Package",
  "Title": "Damsel: an end to end analysis of DamID",
  "Version": "1.9.0",
  "Authors@R": "person(\"Caitlin\", \"Page\", \nemail = \"caitlin.page@petermac.org\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0004-7949-8143\"))",
  "Description": "Damsel provides an end to end analysis of DamID data.\nDamsel takes bam files from Dam-only control and fusion samples\nand counts the reads matching to each GATC region. edgeR is\nutilised to identify regions of enrichment in the fusion\nrelative to the control. Enriched regions are combined into\npeaks, and are associated with nearby genes. Damsel allows for\nIGV style plots to be built as the results build, inspired by\nggcoverage, and using the functionality and layering ability of\nggplot2. Damsel also conducts gene ontology testing with bias\ncorrection through goseq, and future versions of Damsel will\nalso incorporate motif enrichment analysis. Overall, Damsel is\nthe first package allowing for an end to end analysis with\nvisual capabilities. The goal of Damsel was to bring all the\nanalysis into one place, and allow for exploratory analysis\nwithin R.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Config/testthat/edition": "3",
  "RoxygenNote": "7.3.1",
  "BugReports": "https://github.com/Oshlack/Damsel",
  "URL": "https://github.com/Oshlack/Damsel",
  "biocViews": "DifferentialMethylation, PeakDetection, GenePrediction,\nGeneSetEnrichment",
  "VignetteBuilder": "knitr",
  "LazyData": "FALSE",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev perl xz-utils\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:55 UTC",
  "RemoteUrl": "https://github.com/bioc/Damsel",
  "RemoteRef": "HEAD",
  "RemoteSha": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-08 05:30:36 UTC",
    "User": "root"
  },
  "Author": "Caitlin Page [aut, cre] (ORCID:\n<https://orcid.org/0009-0004-7949-8143>)",
  "Maintainer": "Caitlin Page <caitlin.page@petermac.org>",
  "_user": "bioc",
  "_type": "src",
  "_file": "Damsel_1.9.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/cac46267638e8573962b3d5f473fb5d08303de90b60aed6a3455b884673a7755",
  "_filesize": 1695620,
  "_sha256": "cac46267638e8573962b3d5f473fb5d08303de90b60aed6a3455b884673a7755",
  "_expires": "2026-10-16T05:40:34.000Z",
  "_created": "2026-07-08T05:30:36.000Z",
  "_published": "2026-07-08T05:40:36.482Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595",
  "_status": "failure",
  "_upstream": "https://github.com/bioc/Damsel",
  "_commit": {
    "id": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381375
  },
  "_maintainer": {
    "name": "Caitlin Page",
    "email": "caitlin.page@petermac.org",
    "login": "caitlinpage",
    "description": "",
    "uuid": 100269204
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85794738183,
      "time": 332,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8159130516"
    },
    {
      "job": 85794738191,
      "time": 558,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8159186849"
    },
    {
      "job": 85794738219,
      "time": 536,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8159181561"
    },
    {
      "job": 85794738232,
      "time": 380,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8159146077"
    },
    {
      "job": 85794738177,
      "time": 397,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8159149120"
    },
    {
      "job": 85793607254,
      "time": 538,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8159044230"
    },
    {
      "job": 85794738158,
      "time": 290,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8159119673"
    },
    {
      "job": 85794738263,
      "time": 409,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8159150299"
    },
    {
      "job": 85794738212,
      "time": 403,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8159147995"
    },
    {
      "job": 85794738239,
      "time": 436,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8159156614"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "ggbio",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "goseq",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "plyranges",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "Rsubread",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "biomaRt",
      "role": "Suggests"
    },
    {
      "package": "biovizBase",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Dmelanogaster.UCSC.dm6",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "org.Dm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Dmelanogaster.UCSC.dm6.ensGene",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "differentialmethylation",
    "peakdetection",
    "geneprediction",
    "genesetenrichment"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "caitlinpage",
      "count": 405,
      "uuid": 100269204
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    },
    {
      "user": "lonsbio",
      "count": 1,
      "uuid": 2631592
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 268,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Damsel"
  },
  "_devurl": "https://github.com/oshlack/damsel",
  "_searchresults": 21,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/Damsel.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/oshlack/damsel",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "%>%",
    "annotatePeaksGenes",
    "collateGenes",
    "countBamInGATC",
    "geom_dm",
    "geom_gatc",
    "geom_genes_tx",
    "geom_peak",
    "getGatcRegions",
    "identifyPeaks",
    "makeDGE",
    "plotCorrHeatmap",
    "plotCounts",
    "plotCountsDistribution",
    "plotCountsInPeaks",
    "plotGeneOntology",
    "plotWrap",
    "random_counts",
    "random_edgeR_results",
    "random_regions",
    "testDmRegions",
    "testGeneOntology"
  ],
  "_datasets": [
    {
      "name": "dros_counts",
      "title": "Example Drosophila DamID counts",
      "object": "dros_counts",
      "file": "dros_counts.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X",
        "Position",
        "seqnames",
        "start",
        "end",
        "width",
        "strand",
        "dam_1_SRR7948872.BAM",
        "sd_1_SRR7948874.BAM",
        "dam_2_SRR7948876.BAM",
        "sd_2_SRR7948877.BAM"
      ],
      "rows": 80000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "annotatePeaksGenes",
      "title": "Annotation of peaks and genes",
      "topics": [
        "annotatePeaksGenes"
      ]
    },
    {
      "page": "collateGenes",
      "title": "Get list of genes",
      "topics": [
        "collateGenes"
      ]
    },
    {
      "page": "countBamInGATC",
      "title": "Obtain region counts for BAM files",
      "topics": [
        "countBamInGATC"
      ]
    },
    {
      "page": "dros_counts",
      "title": "Example Drosophila DamID counts",
      "topics": [
        "dros_counts"
      ]
    },
    {
      "page": "geom_dm",
      "title": "Plotting results from differential methylation testing",
      "topics": [
        "geom_dm"
      ]
    },
    {
      "page": "geom_gatc",
      "title": "Plot for a GATC track",
      "topics": [
        "geom_gatc"
      ]
    },
    {
      "page": "geom_genes_tx",
      "title": "Plotting genes",
      "topics": [
        "geom_genes_tx"
      ]
    },
    {
      "page": "geom_peak",
      "title": "Plotting peaks",
      "topics": [
        "geom_peak"
      ]
    },
    {
      "page": "getGatcRegions",
      "title": "Extract GATC regions",
      "topics": [
        "getGatcRegions"
      ]
    },
    {
      "page": "identifyPeaks",
      "title": "Identify peaks from differentially methylated regions",
      "topics": [
        "identifyPeaks"
      ]
    },
    {
      "page": "makeDGE",
      "title": "Create DGE object for differential testing",
      "topics": [
        "makeDGE"
      ]
    },
    {
      "page": "plotCorrHeatmap",
      "title": "Plot correlation heatmap",
      "topics": [
        "plotCorrHeatmap"
      ]
    },
    {
      "page": "plotCounts",
      "title": "Plot for counts for all samples across a given region",
      "topics": [
        "plotCounts"
      ]
    },
    {
      "page": "plotCountsDistribution",
      "title": "Plot distribution of counts `plotCountsDistribution` plots the distribution of counts enabling the comparison of different samples. Can highlight the different library sizes of the samples.",
      "topics": [
        "plotCountsDistribution"
      ]
    },
    {
      "page": "plotCountsInPeaks",
      "title": "Plotting the",
      "topics": [
        "plotCountsInPeaks"
      ]
    },
    {
      "page": "plotGeneOntology",
      "title": "Plot gene ontology results",
      "topics": [
        "plotGeneOntology"
      ]
    },
    {
      "page": "plotWrap",
      "title": "Wrapper function for plotting",
      "topics": [
        "plotWrap"
      ]
    },
    {
      "page": "random_counts",
      "title": "Create example counts",
      "topics": [
        "random_counts"
      ]
    },
    {
      "page": "random_edgeR_results",
      "title": "Create example edgeR results",
      "topics": [
        "random_edgeR_results"
      ]
    },
    {
      "page": "random_regions",
      "title": "Create example regions",
      "topics": [
        "random_regions"
      ]
    },
    {
      "page": "testDmRegions",
      "title": "Differential testing",
      "topics": [
        "testDmRegions"
      ]
    },
    {
      "page": "testGeneOntology",
      "title": "Gene ontology analysis",
      "topics": [
        "testGeneOntology"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Damsel/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "BiasedUrn",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "checkmate",
    "cigarillo",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dichromat",
    "digest",
    "doParallel",
    "dplyr",
    "edgeR",
    "ensembldb",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreach",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "geneLenDataBase",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GetoptLong",
    "ggbio",
    "ggplot2",
    "GlobalOptions",
    "glue",
    "GO.db",
    "goseq",
    "graph",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "nlme",
    "nnet",
    "openssl",
    "OrganismDbi",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plyr",
    "plyranges",
    "png",
    "prettyunits",
    "progress",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "Rsubread",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "txdbmaker",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_score": 3.623249290397901,
  "_indexed": true,
  "_nocasepkg": "damsel",
  "_universes": [
    "bioc",
    "caitlinpage",
    "oshlack"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-07-08T05:36:32.000Z",
      "distro": "resolute",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/b97046410001afe2c3609ccbb27d3ae553e97dd51074ca19cf3b19163681a99b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-07-08T05:36:43.000Z",
      "distro": "resolute",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/d22e36c231881946977d1112213ecc0b114eb1d696aa33f0bde9375c9e580d1d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-07-08T05:33:38.000Z",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/aae4fea02811ad68dfc82db414eafc69c6399707e02ea62886d8b1990c0e77a3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-07-08T05:34:02.000Z",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/4c018edb84c69c09d44b01f971b98ad18c8659accde1730be9b7cc0833e2863d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.0",
      "date": "2026-07-08T05:35:47.000Z",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/e80064bc7b9b228b8773f13c1cb5d932e9f5267e75c1b172464b34f816c63514",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-07-08T05:34:52.000Z",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/3b6f60286687bad83ee615b77be41fd1f9d63223c32f3752b2ac2714a05ab394",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-07-08T05:34:21.000Z",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/be7c7d8b9735dd7a128c1bf6717fb4c40640613e81fdba4eb55019e8b37defdd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-07-08T05:34:48.000Z",
      "commit": "08681dc37149314a9e4a0f841b77e7c95d10f52c",
      "fileid": "https://r2.ropensci.org/8cf39e987ae0324875e714499ec6882ba494ba755d9edb8f4b70a4bed2e6dc11",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919558595"
    }
  ]
}