{
  "_id": "6aabc61e3d719c1f8406e876",
  "Package": "Trendy",
  "Type": "Package",
  "Title": "Breakpoint analysis of time-course expression data",
  "Version": "1.34.0",
  "Author": "Rhonda Bacher and Ning Leng",
  "Maintainer": "Rhonda Bacher <rbacher@ufl.edu>",
  "Description": "Trendy implements segmented (or breakpoint) regression\nmodels to estimate breakpoints which represent changes in\nexpression for each feature/gene in high throughput data with\nordered conditions.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.1.1",
  "VignetteBuilder": "knitr",
  "biocViews": "TimeCourse, RNASeq, Regression, ImmunoOncology",
  "URL": "https://github.com/rhondabacher/Trendy",
  "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:47:11 UTC",
  "RemoteUrl": "https://github.com/bioc/Trendy",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "f0d057e1380ea0781987b72e815155ec5ed74487",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-17 09:46:43 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "Trendy_1.34.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d0608591e588af563888e096c3ac0d17ed433ebdd411672bc3fa4bd336596ccd",
  "_filesize": 1254401,
  "_sha256": "d0608591e588af563888e096c3ac0d17ed433ebdd411672bc3fa4bd336596ccd",
  "_expires": "2026-12-26T10:51:08.000Z",
  "_created": "2026-09-17T09:46:43.000Z",
  "_published": "2026-09-17T10:51:10.829Z",
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 12
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798",
  "_status": "success",
  "_upstream": "https://github.com/bioc/Trendy",
  "_commit": {
    "id": "f0d057e1380ea0781987b72e815155ec5ed74487",
    "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": 1777380431
  },
  "_maintainer": {
    "name": "Rhonda Bacher",
    "email": "rbacher@ufl.edu",
    "login": "rhondabacher",
    "twitter": "@rbacher",
    "description": "Associate Professor of Biostatistics at the University of Florida",
    "uuid": 6611436
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 105155186039,
      "time": 200,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "10490590710"
    },
    {
      "job": 105155185997,
      "time": 370,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10491060128"
    },
    {
      "job": 105155185985,
      "time": 329,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10490915527"
    },
    {
      "job": 105155186035,
      "time": 175,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10494475103"
    },
    {
      "job": 105155186008,
      "time": 197,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10493266138"
    },
    {
      "job": 105153366352,
      "time": 364,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10489704036"
    },
    {
      "job": 105155186007,
      "time": 162,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10490471136"
    },
    {
      "job": 105155186251,
      "time": 238,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10491070073"
    },
    {
      "job": 105155185994,
      "time": 222,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10490189008"
    },
    {
      "job": 105155186006,
      "time": 167,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10490580659"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "segmented",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinyFiles",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "timecourse",
    "rnaseq",
    "regression",
    "immunooncology"
  ],
  "_stars": 7,
  "_contributors": [
    {
      "user": "rhondabacher",
      "count": 145,
      "uuid": 6611436
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "lengning",
      "count": 8,
      "uuid": 11322800
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    },
    {
      "user": "link-ny",
      "count": 2,
      "uuid": 4392950
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 554,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Trendy"
  },
  "_mentions": 8,
  "_devurl": "https://github.com/rhondabacher/trendy",
  "_searchresults": 20,
  "_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/Trendy.html"
  ],
  "_homeurl": "https://github.com/rhondabacher/trendy",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "breakpointDist",
    "breakpointFit",
    "extractPattern",
    "fitSegBIC",
    "formatFunc",
    "formatResults",
    "getCounts",
    "plotFeature",
    "results",
    "topTrendy",
    "trendHeatmap",
    "trendy",
    "trendyShiny"
  ],
  "_datasets": [
    {
      "name": "trendyExampleData",
      "title": "Example dataset for Trendy",
      "object": "trendyExampleData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "s1",
        "s2",
        "s3",
        "s4",
        "s5",
        "s6",
        "s7",
        "s8",
        "s9",
        "s10",
        "s11",
        "s12",
        "s13",
        "s14",
        "s15",
        "s16",
        "s17",
        "s18",
        "s19",
        "s20",
        "s21",
        "s22",
        "s23",
        "s24",
        "s25",
        "s26",
        "s27",
        "s28",
        "s29",
        "s30",
        "s31",
        "s32",
        "s33",
        "s34",
        "s35",
        "s36",
        "s37",
        "s38",
        "s39",
        "s40"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "breakpointDist",
      "title": "Distribution of breakpoints",
      "topics": [
        "breakpointDist"
      ]
    },
    {
      "page": "breakpointFit",
      "title": "break point fits",
      "topics": [
        "breakpointFit"
      ]
    },
    {
      "page": "extractPattern",
      "title": "Extract pattern from segmented regression",
      "topics": [
        "extractPattern"
      ]
    },
    {
      "page": "fitSegBIC",
      "title": "Fit segmented regression models on a feature/gene",
      "topics": [
        "fitSegBIC"
      ]
    },
    {
      "page": "formatFunc",
      "title": "internal helper function to format results",
      "topics": [
        "formatFunc"
      ]
    },
    {
      "page": "formatResults",
      "title": "Function to format results for saving.",
      "topics": [
        "formatResults"
      ]
    },
    {
      "page": "getCounts",
      "title": "getCounts",
      "topics": [
        "getCounts"
      ]
    },
    {
      "page": "plotFeature",
      "title": "Plot features of interest",
      "topics": [
        "plotFeature"
      ]
    },
    {
      "page": "results",
      "title": "results",
      "topics": [
        "results"
      ]
    },
    {
      "page": "topTrendy",
      "title": "obtain top genes from trendy results",
      "topics": [
        "topTrendy"
      ]
    },
    {
      "page": "trendHeatmap",
      "title": "Draw heatmap of gene expression trends",
      "topics": [
        "trendHeatmap"
      ]
    },
    {
      "page": "trendy",
      "title": "Trendy",
      "topics": [
        "trendy"
      ]
    },
    {
      "page": "trendyExampleData",
      "title": "Example dataset for Trendy",
      "topics": [
        "trendyExampleData"
      ]
    },
    {
      "page": "trendyShiny",
      "title": "Trendy shiny app to interactively vizualize results after running trendy().",
      "topics": [
        "trendyShiny"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Trendy/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "codetools",
    "commonmark",
    "cpp11",
    "crosstalk",
    "DelayedArray",
    "digest",
    "DT",
    "evaluate",
    "fastmap",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "gplots",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "IRanges",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nlme",
    "otel",
    "pillar",
    "pkgconfig",
    "promises",
    "R6",
    "rappdirs",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "sass",
    "segmented",
    "Seqinfo",
    "shiny",
    "shinyFiles",
    "snow",
    "sourcetools",
    "SparseArray",
    "SummarizedExperiment",
    "tibble",
    "tinytex",
    "utf8",
    "vctrs",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "Trendy_vignette.Rnw",
      "filename": "Trendy_vignette.pdf",
      "title": "Trendy Vignette",
      "engine": "knitr::knitr",
      "headings": [
        "1 Overview",
        "2 Installation",
        "3 Analysis",
        "4 More advanced analysis",
        "5 Trendy shiny app",
        "6 SessionInfo"
      ],
      "created": "2018-01-08 17:30:28",
      "modified": "2019-11-13 18:09:34",
      "commits": 16
    }
  ],
  "_score": 7.225309281725863,
  "_indexed": false,
  "_nocasepkg": "trendy",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/Trendy",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.34.0",
      "date": "2026-09-17T09:51:07.000Z",
      "distro": "resolute",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/a6c2b917db7fdc823b6418ea9321772b58c5f61bafbbe7b1373ae93bb19d5265",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.34.0",
      "date": "2026-09-17T09:50:52.000Z",
      "distro": "resolute",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/9a0c9af6ddaeb38cae59a8e5ca186010535417d848d0a13776c3c0fa1ba7b4a1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.34.0",
      "date": "2026-09-17T10:49:18.000Z",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/6c71c00f5817be3ae67e6e4fc3e084203b0e263aabb16690a40635af272e8b07",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.34.0",
      "date": "2026-09-17T10:48:53.000Z",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/4227adb18e4d6b53213e471072eaaa13b9ac5e832d0f6fed5397862f041e78bc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.34.0",
      "date": "2026-09-17T09:49:57.000Z",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/ef771ec069517f3c8f3bc8301f3acd8752b13f45a0028a58efb794619ee55429",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-09-17T09:48:53.000Z",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/e8d833e3acb065fd560142cbb8cd972691a6f829588549c771bd5e5df36824ac",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-09-17T09:48:29.000Z",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/26b99ee2bc61626b447f0a259555348ef3c90158a87f1c26500856d9dc18ea33",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.34.0",
      "date": "2026-09-17T09:48:24.000Z",
      "commit": "f0d057e1380ea0781987b72e815155ec5ed74487",
      "fileid": "https://r2.ropensci.org/779c571aa23bdc4b8cc87afa6e256d78da049b2f96eb9e5c2503332ef6133efb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35206422798"
    }
  ]
}