{
  "_id": "6a57f584ff0138dec5d72341",
  "Package": "atena",
  "Type": "Package",
  "Title": "Analysis of Transposable Elements",
  "Version": "1.19.1",
  "Authors@R": "c(\nperson(\"Beatriz\", \"Calvo-Serra\", email=\"beatriz.calvo@upf.edu\",\nrole=c(\"aut\")),\nperson(\"Robert\", \"Castelo\", email=\"robert.castelo@upf.edu\",\nrole=c(\"aut\", \"cre\")))",
  "Description": "Quantify expression of transposable elements (TEs) from\nRNA-seq data through different methods, including ERVmap,\nTEtranscripts and Telescope. A common interface is provided to\nuse each of these methods, which consists of building a\nparameter object, calling the quantification function with this\nobject and getting a SummarizedExperiment object as output\ncontainer of the quantified expression profiles. The\nimplementation allows one to quantify TEs and gene transcripts\nin an integrated manner.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "biocViews": "Transcription, Transcriptomics, RNASeq, Sequencing,\nPreprocessing, Software, GeneExpression, Coverage,\nDifferentialExpression, FunctionalGenomics",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/rcastelo/atena",
  "BugReports": "https://github.com/rcastelo/atena/issues",
  "Collate": "'AllGenerics.R' 'AllClasses.R' 'ERVmap.R' 'TEtranscripts.R'\n'Telescope.R' 'annotations.R' 'atena.R' 'atenaMethod.R'\n'overlappingModes.R' 'qtex.R' 'utils.R' 'zzz.R'",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-15 16:20:45 UTC",
  "RemoteUrl": "https://github.com/bioc/atena",
  "RemoteRef": "HEAD",
  "RemoteSha": "afce0c7b8e5492a351128b447496e4546711057d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-15 20:56:13 UTC",
    "User": "root"
  },
  "Author": "Beatriz Calvo-Serra [aut],\nRobert Castelo [aut, cre]",
  "Maintainer": "Robert Castelo <robert.castelo@upf.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "atena_1.19.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/1076a0f9fbb44a6e30263733dcb1544f340d0380cbef8c1baadd454e6333a1a7",
  "_filesize": 1261013,
  "_sha256": "1076a0f9fbb44a6e30263733dcb1544f340d0380cbef8c1baadd454e6333a1a7",
  "_expires": "2026-10-23T21:02:57.000Z",
  "_created": "2026-07-15T20:56:13.000Z",
  "_published": "2026-07-15T21:02:59.919Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 13
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690",
  "_status": "success",
  "_upstream": "https://github.com/bioc/atena",
  "_commit": {
    "id": "afce0c7b8e5492a351128b447496e4546711057d",
    "author": "Robert Castelo <robert.castelo@upf.edu>",
    "committer": "Robert Castelo <robert.castelo@upf.edu>",
    "message": "Replace defunct call GenomicAlignments::explodeCigarOplengths() by new cigarillo::explode_cigar_oplens()\n",
    "time": 1784132445
  },
  "_maintainer": {
    "name": "Robert Castelo",
    "email": "robert.castelo@upf.edu",
    "login": "rcastelo",
    "twitter": "@robertclab",
    "description": "biostatistics, machine learning, genetics, genomics, R/Bioconductor",
    "uuid": 1677433
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 87470495777,
      "time": 257,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8357239284"
    },
    {
      "job": 87470495779,
      "time": 306,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8357258485"
    },
    {
      "job": 87470495787,
      "time": 332,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8357267719"
    },
    {
      "job": 87470495753,
      "time": 137,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8357192497"
    },
    {
      "job": 87470495790,
      "time": 178,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8357208507"
    },
    {
      "job": 87467851209,
      "time": 805,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8357138830"
    },
    {
      "job": 87470495736,
      "time": 196,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8357215016"
    },
    {
      "job": 87470495744,
      "time": 138,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8357193464"
    },
    {
      "job": 87470495786,
      "time": 148,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8357197063"
    },
    {
      "job": 87470495766,
      "time": 174,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8357206927"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "MatrixGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "SQUAREM",
      "role": "Imports"
    },
    {
      "package": "sparseMatrixStats",
      "role": "Imports"
    },
    {
      "package": "AnnotationHub",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Dmelanogaster.UCSC.dm6.ensGene",
      "role": "Suggests"
    },
    {
      "package": "RColorBrewer",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-43",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 3
    },
    {
      "week": "2026-29",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.19.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.18.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "transcription",
    "transcriptomics",
    "rnaseq",
    "sequencing",
    "preprocessing",
    "software",
    "geneexpression",
    "coverage",
    "differentialexpression",
    "functionalgenomics"
  ],
  "_stars": 14,
  "_contributors": [
    {
      "user": "beacalvo",
      "count": 262,
      "uuid": 45432116
    },
    {
      "user": "rcastelo",
      "count": 54,
      "uuid": 1677433
    },
    {
      "user": "pablo-rodr-bio2",
      "count": 16,
      "uuid": 53177189
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    },
    {
      "user": "petehaitch",
      "count": 3,
      "uuid": 1049741
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 447,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 461,
    "source": "https://www.bioconductor.org/packages/stats/bioc/atena"
  },
  "_devurl": "https://github.com/rcastelo/atena",
  "_searchresults": 4,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/atena.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/rcastelo/atena",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "annotaTEs",
    "atenaParam",
    "ERVmapParam",
    "features",
    "getDNAtransposons",
    "getLINEs",
    "getLTRs",
    "getSINEs",
    "OneCodeToFindThemAll",
    "ovIntersectionStrict",
    "ovUnion",
    "path",
    "qtex",
    "rmskatenaparser",
    "rmskbasicparser",
    "rmskidentity",
    "show",
    "TelescopeParam",
    "TEtranscriptsParam"
  ],
  "_help": [
    {
      "page": "atena-package",
      "title": "atena: analysis of transposable elements in R and Bioconductor",
      "topics": [
        "atena-package",
        "atena"
      ]
    },
    {
      "page": "annotaTEs",
      "title": "Get RepeatMasker UCSC annotations",
      "topics": [
        "annotaTEs"
      ]
    },
    {
      "page": "annotaTEsGetters",
      "title": "Getter functions of TE classes from parsed RepeatMasker annotations.",
      "topics": [
        "annotateTEsGetters",
        "getDNAtransposons",
        "getLINEs",
        "getLTRs",
        "getSINEs"
      ]
    },
    {
      "page": "atenaParam-class",
      "title": "atena parameter class",
      "topics": [
        "atenaParam",
        "atenaParam-class",
        "show,atenaParam-method"
      ]
    },
    {
      "page": "ERVmapParam-class",
      "title": "ERVmap parameter class",
      "topics": [
        "ERVmapParam",
        "ERVmapParam-class",
        "show,ERVmapParam-method"
      ]
    },
    {
      "page": "OneCodeToFindThemAll",
      "title": "OneCodeToFindThemAll parser of RepeatMasker annotations",
      "topics": [
        "OneCodeToFindThemAll"
      ]
    },
    {
      "page": "ovFunctions",
      "title": "Pre-defined overlapping mode functions",
      "topics": [
        "ovIntersectionStrict",
        "ovUnion"
      ]
    },
    {
      "page": "qtex",
      "title": "Quantify transposable element expression",
      "topics": [
        "qtex",
        "qtex,AtenaParam-method",
        "qtex,atenaParam-method",
        "qtex,ERVmapParam-method",
        "qtex,TelescopeParam-method",
        "qtex,TEtranscriptsParam-method"
      ]
    },
    {
      "page": "QuantifyParam-class",
      "title": "QuantifyParam parameter class",
      "topics": [
        "features,QuantifyParam-method",
        "path,QuantifyParam-method",
        "QuantifyParam-class"
      ]
    },
    {
      "page": "rmskatenaparser",
      "title": "atena annotation parser of RepeatMasker annotations",
      "topics": [
        "rmskatenaparser"
      ]
    },
    {
      "page": "rmskbasicparser",
      "title": "Parser of RepeatMasker annotations",
      "topics": [
        "rmskbasicparser"
      ]
    },
    {
      "page": "rmskidentity",
      "title": "Identity function for parsefun",
      "topics": [
        "rmskidentity"
      ]
    },
    {
      "page": "TelescopeParam-class",
      "title": "Telescope parameter class",
      "topics": [
        "show,TelescopeParam-method",
        "TelescopeParam",
        "TelescopeParam-class"
      ]
    },
    {
      "page": "TEtranscriptsParam-class",
      "title": "TEtranscripts parameter class",
      "topics": [
        "show,TEtranscriptsParam-method",
        "TEtranscriptsParam",
        "TEtranscriptsParam-class"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/atena/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "httr",
    "httr2",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "rappdirs",
    "Rcpp",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "SQUAREM",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "atena.Rmd",
      "filename": "atena.html",
      "title": "An introduction to the atena package",
      "author": "Beatriz Calvo-Serra, Robert Castelo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What are transposable elements",
        "Currently available methods for quantifying TE expression",
        "TEs annotations",
        "Retrieving and parsing TE annotations",
        "TE expression quantification",
        "Building a parameter object",
        "ERVmap",
        "Telescope",
        "TEtranscripts",
        "Quantifying expression",
        "Accesing expression quantifications and metadata",
        "Session information",
        "References"
      ],
      "created": "2021-02-02 12:02:45",
      "modified": "2024-04-24 07:12:58",
      "commits": 34
    }
  ],
  "_score": 6.243038048686294,
  "_indexed": true,
  "_nocasepkg": "atena",
  "_universes": [
    "bioc",
    "rcastelo"
  ],
  "_previous": "1.19.0",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.19.1",
      "date": "2026-07-15T21:01:45.000Z",
      "distro": "resolute",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/5e80d3a0f0e18af245b1b9b150cf9c61773ece1a3ecdfae36932eb5864fabe98",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.19.1",
      "date": "2026-07-15T21:02:13.000Z",
      "distro": "resolute",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/fdd9415b92ce3192f542261f157b4d27555aeb3ce3c04c9b0bb67e7205c02c56",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.19.1",
      "date": "2026-07-15T20:59:00.000Z",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/b4f7889237e5c20ef3c7186af0d5e5176b375987be82dccc35d82883c8ab24f0",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.19.1",
      "date": "2026-07-15T20:59:37.000Z",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/b7bddbe89e5f2357101a9ce1dfbce825bccec215ee97a565f0cf6861e68d31e4",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.19.1",
      "date": "2026-07-15T21:00:19.000Z",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/22c58ab8a914119199212bcfd5b8adbff118431473b4a29f985919672549dc93",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.19.1",
      "date": "2026-07-15T20:58:57.000Z",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/af1919023439266dfa9467a172c80babfeb19a5e698a672c8f22b395a5f264bc",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.19.1",
      "date": "2026-07-15T20:59:04.000Z",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/1d60f0a7eb75a114a16b67f69cffac2ca607524ac90f43044a6792fdec47169c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.19.1",
      "date": "2026-07-15T20:59:20.000Z",
      "commit": "afce0c7b8e5492a351128b447496e4546711057d",
      "fileid": "https://r2.ropensci.org/9ca96488d7f2dd3f31dd58d4986e9db3d5d7e6d7d8a264915bd878c4d6856560",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29449371690"
    }
  ]
}