{
  "_id": "6ac0b4dc91601a2ad2997a68",
  "Package": "TRESS",
  "Type": "Package",
  "Title": "Toolbox for mRNA epigenetics sequencing analysis",
  "Version": "1.18.0",
  "Authors@R": "c(person(given = \"Zhenxing\",\nfamily = \"Guo\",\nrole = c(\"aut\", \"cre\"),\nemail = \"guozhenxing@cuhk.edu.cn\"),\nperson(given = \"Hao\",\nfamily = \"Wu\",\nrole = \"ctb\"))",
  "Description": "This package is devoted to analyzing MeRIP-seq data.\nCurrent functionalities include 1. detect transcriptome wide\nm6A methylation regions 2. detect transcriptome wide\ndifferential m6A methylation regions.",
  "biocViews": "Epigenetics, RNASeq, PeakDetection, DifferentialMethylation",
  "License": "GPL-3 + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.1.1",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:57:10 UTC",
  "RemoteUrl": "https://github.com/bioc/TRESS",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "e39fed188b2aa38f800d314021bff2b4836f20c9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-03 07:47:18 UTC",
    "User": "root"
  },
  "Author": "Zhenxing Guo [aut, cre],\nHao Wu [ctb]",
  "Maintainer": "Zhenxing Guo <guozhenxing@cuhk.edu.cn>",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "TRESS_1.18.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b2ef01116a1f360767eb19d52171bbb08b1617f47e1a02ec4f776346b1347bff",
  "_filesize": 716590,
  "_sha256": "b2ef01116a1f360767eb19d52171bbb08b1617f47e1a02ec4f776346b1347bff",
  "_expires": "2027-01-11T07:55:07.000Z",
  "_created": "2026-10-03T07:47:18.000Z",
  "_published": "2026-10-03T07:55:08.854Z",
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 15
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561",
  "_status": "success",
  "_upstream": "https://github.com/bioc/TRESS",
  "_commit": {
    "id": "e39fed188b2aa38f800d314021bff2b4836f20c9",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777381030
  },
  "_maintainer": {
    "name": "Zhenxing Guo",
    "email": "guozhenxing@cuhk.edu.cn",
    "login": "zhenxingguo0015",
    "description": "",
    "uuid": 58897867
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 111158937699,
      "time": 183,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11268876122"
    },
    {
      "job": 111158937764,
      "time": 403,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11268277723"
    },
    {
      "job": 111158937761,
      "time": 386,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11268372343"
    },
    {
      "job": 111158937736,
      "time": 244,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11268297552"
    },
    {
      "job": 111158937718,
      "time": 276,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11268656887"
    },
    {
      "job": 111158303445,
      "time": 233,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11267949022"
    },
    {
      "job": 111158937704,
      "time": 113,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11268591681"
    },
    {
      "job": 111158937726,
      "time": 359,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11268104348"
    },
    {
      "job": 111158937723,
      "time": 307,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11268651927"
    },
    {
      "job": 111158937786,
      "time": 349,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11267659623"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "parallel",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.19.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.18.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "epigenetics",
    "rnaseq",
    "peakdetection",
    "differentialmethylation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 421,
    "source": "https://www.bioconductor.org/packages/stats/bioc/TRESS"
  },
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/TRESS.html",
    "LICENSE"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CallCandidates",
    "CallDMRs.paramEsti",
    "CallPeaks.multiRep",
    "CallPeaks.oneRep",
    "CallPeaks.paramEsti",
    "CoefName",
    "DivideBins",
    "DMRInfer",
    "filterRegions",
    "findBumps",
    "meRatio",
    "ShowOnePeak",
    "TRESS_DMRfit",
    "TRESS_DMRtest",
    "TRESS_peak"
  ],
  "_datasets": [
    {
      "name": "Basal",
      "title": "Bin-level and region-level data from basal mouse brain samples",
      "object": "Basal",
      "file": "Basal.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DMR_M3vsWT",
      "title": "Transcriptome location and read counts of 200 candidate DMRs, and size factors.",
      "object": "DMR_M3vsWT",
      "file": "DMR_M3vsWT.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "DMR_SixWeekvsTwoWeek",
      "title": "Transcriptome location and read counts of 200 candidate DMRs.",
      "object": "DMR_SixWeekvsTwoWeek",
      "file": "DMR_SixWeekvsTwoWeek.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Basal",
      "title": "Bin-level and region-level data from basal mouse brain samples",
      "topics": [
        "Basal"
      ]
    },
    {
      "page": "CallCandidates",
      "title": "Call candidate m6A regions or candidate differential m6A regions.",
      "topics": [
        "CallCandidates"
      ]
    },
    {
      "page": "CallDMRs.paramEsti",
      "title": "Model fitting and parameter estimation by TRESS for each candidate DMR.",
      "topics": [
        "CallDMRs.paramEsti"
      ]
    },
    {
      "page": "CallPeaks.multiRep",
      "title": "m6A peak calling with multiple replicates.",
      "topics": [
        "CallPeaks.multiRep"
      ]
    },
    {
      "page": "CallPeaks.oneRep",
      "title": "m6A peak calling with only one replicate.",
      "topics": [
        "CallPeaks.oneRep"
      ]
    },
    {
      "page": "CallPeaks.paramEsti",
      "title": "Parameter estimation in m6A peak calling with multiple replicates.",
      "topics": [
        "CallPeaks.paramEsti"
      ]
    },
    {
      "page": "CoefName",
      "title": "Obtain the name of each coefficient in design matrix.",
      "topics": [
        "CoefName"
      ]
    },
    {
      "page": "DivideBins",
      "title": "Obtain genomic bins and bin-level read counts from BAM files.",
      "topics": [
        "DivideBins"
      ]
    },
    {
      "page": "DMR_M3vsWT",
      "title": "Transcriptome location and read counts of 200 candidate DMRs, and size factors.",
      "topics": [
        "DMR_M3vsWT"
      ]
    },
    {
      "page": "DMR_SixWeekvsTwoWeek",
      "title": "Transcriptome location and read counts of 200 candidate DMRs.",
      "topics": [
        "DMR_SixWeekvsTwoWeek"
      ]
    },
    {
      "page": "DMRInfer",
      "title": "P-value calculation given Wald statistics.",
      "topics": [
        "DMRInfer"
      ]
    },
    {
      "page": "filterRegions",
      "title": "Pre-filtering of candidate DMRs.",
      "topics": [
        "filterRegions"
      ]
    },
    {
      "page": "findBumps",
      "title": "Bump-finding from transcriptome bins.",
      "topics": [
        "findBumps"
      ]
    },
    {
      "page": "meRatio",
      "title": "Observed m6A methylation ratio.",
      "topics": [
        "meRatio"
      ]
    },
    {
      "page": "ShowOnePeak",
      "title": "Visulization of a single peak along the genome.",
      "topics": [
        "ShowOnePeak"
      ]
    },
    {
      "page": "TRESS_DMRfit",
      "title": "Differential m6A methylation analysis for MeRIP-seq data under general experimental design",
      "topics": [
        "TRESS_DMRfit"
      ]
    },
    {
      "page": "TRESS_DMRtest",
      "title": "Hypothesis testing on candidate DMRs.",
      "topics": [
        "TRESS_DMRtest"
      ]
    },
    {
      "page": "TRESS_peak",
      "title": "Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing.",
      "topics": [
        "TRESS_peak"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/TRESS/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "vctrs",
    "XML",
    "XVector",
    "yaml"
  ],
  "_score": 3.4771212547196626,
  "_indexed": false,
  "_nocasepkg": "tress",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/TRESS",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-03T07:51:08.000Z",
      "distro": "resolute",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/683aa24cc98ef188a654d0f52304ba1bfa1ee5a09c638e8bed5d2984d66ba7c1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.18.0",
      "date": "2026-10-03T07:50:59.000Z",
      "distro": "resolute",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/5098792a1aec672acc66edf521d18adbcc18b635fdf6f162aa3a796d8bdd8f89",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.18.0",
      "date": "2026-10-03T07:49:39.000Z",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/cea8d1461df15afb083d4df9d9377984ece9f546cd0889119cc4588d42245e5c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.18.0",
      "date": "2026-10-03T07:49:34.000Z",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/972eebb4f42d9ac583350855b4dc890050ce05af78c736a79dee7ea3c0c6f755",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.18.0",
      "date": "2026-10-03T07:49:53.000Z",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/e66ecb3674919d14ed9d8cd8dc9c86cb69ac11098d76695bb960aed8cf54db1d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.18.0",
      "date": "2026-10-03T07:49:49.000Z",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/b90354b142db3e72cd3271c41681e59c021088b594f886167f43c15257bacb4a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.18.0",
      "date": "2026-10-03T07:49:47.000Z",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/1b69efc34bae9ca388e799d3d890647ae476822bf1af2dfe93bf5db56e683379",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.18.0",
      "date": "2026-10-03T07:49:25.000Z",
      "commit": "e39fed188b2aa38f800d314021bff2b4836f20c9",
      "fileid": "https://r2.ropensci.org/dafef3743ce28ab716cd7da0c65b7fe76a03fb719b3148b4cd47a24c3ed2504b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37107304561"
    }
  ]
}