{
  "_id": "6a1aa9521d7bb097a09d4d0d",
  "Package": "RolDE",
  "Type": "Package",
  "Title": "RolDE: Robust longitudinal Differential Expression",
  "Version": "1.17.0",
  "Description": "RolDE detects longitudinal differential expression between\ntwo conditions in noisy high-troughput data. Suitable even for\ndata with a moderate amount of missing values.RolDE is a\ncomposite method, consisting of three independent modules with\ndifferent approaches to detecting longitudinal differential\nexpression. The combination of these diverse modules allows\nRolDE to robustly detect varying differences in longitudinal\ntrends and expression levels in diverse data types and\nexperimental settings.",
  "Authors@R": "c(person(\"Tommi\", \"Valikangas\", email = \"tsvali@utu.fi\", role=c(\"aut\")),\nperson(\"Medical Bioinformatics Centre\", email = \"mbc@utu.fi\", role=c(\"cre\")))",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "FALSE",
  "RoxygenNote": "7.1.2",
  "VignetteBuilder": "knitr",
  "biocViews": "StatisticalMethod, Software, TimeCourse, Regression,\nProteomics, DifferentialExpression",
  "NeedsCompilation": "no",
  "URL": "https://github.com/elolab/RolDE",
  "BugReports": "https://github.com/elolab/RolDE/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:12 UTC",
  "RemoteUrl": "https://github.com/bioc/RolDE",
  "RemoteRef": "HEAD",
  "RemoteSha": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
  "Packaged": {
    "Date": "2026-05-30 06:54:02 UTC",
    "User": "root"
  },
  "Author": "Tommi Valikangas [aut],\nMedical Bioinformatics Centre [cre]",
  "Maintainer": "Medical Bioinformatics Centre <mbc@utu.fi>",
  "MD5sum": "2b0628e5f1ca2c7e9a7488d220b09fc7",
  "_user": "bioc",
  "_type": "src",
  "_file": "RolDE_1.17.0.tar.gz",
  "_fileid": "49e3e5cdff9f444af641cc23fdcaa1a4d31bf44fb13b78d8d1e5d215f4b3f982",
  "_filesize": 1481136,
  "_sha256": "49e3e5cdff9f444af641cc23fdcaa1a4d31bf44fb13b78d8d1e5d215f4b3f982",
  "_created": "2026-05-30T06:54:02.000Z",
  "_published": "2026-05-30T09:09:38.580Z",
  "_jobs": [
    {
      "job": 78631663168,
      "time": 174,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306254070"
    },
    {
      "job": 78631663202,
      "time": 364,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306275106"
    },
    {
      "job": 78631663184,
      "time": 371,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306276114"
    },
    {
      "job": 78631663170,
      "time": 188,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307060900"
    },
    {
      "job": 78631663166,
      "time": 271,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307067263"
    },
    {
      "job": 78631446097,
      "time": 248,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306235089"
    },
    {
      "job": 78631663169,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306249982"
    },
    {
      "job": 78631663196,
      "time": 301,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306268145"
    },
    {
      "job": 78631663193,
      "time": 248,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306262100"
    },
    {
      "job": 78631663195,
      "time": 311,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306269371"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677310584",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/RolDE",
  "_commit": {
    "id": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
    "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": 1777381092
  },
  "_maintainer": {
    "name": "Medical Bioinformatics Centre",
    "email": "mbc@utu.fi"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ROTS",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "doRNG",
      "role": "Imports"
    },
    {
      "package": "rngtools",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "nlme",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "printr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.16.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "statisticalmethod",
    "software",
    "timecourse",
    "regression",
    "proteomics",
    "differentialexpression"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "jwokaty",
      "count": 14,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    },
    {
      "user": "suomtomi",
      "count": 1,
      "uuid": 32176114
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 359,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RolDE"
  },
  "_devurl": "https://github.com/elolab/rolde",
  "_searchresults": 1,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/RolDE.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/elolab/rolde",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "plotFindings",
    "RolDE",
    "RolDE_Main"
  ],
  "_datasets": [
    {
      "name": "data1",
      "title": "A proteomics dataset with random protein expression values - no missing values.",
      "object": "data1",
      "file": "data1.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Condition1_timepoint_1_Sample_1_r1",
        "Condition1_timepoint_1_Sample_1_r2",
        "Condition1_timepoint_1_Sample_1_r3",
        "Condition1_timepoint_2_Sample_2_r1",
        "Condition1_timepoint_2_Sample_2_r2",
        "Condition1_timepoint_2_Sample_2_r3",
        "Condition1_timepoint_3_Sample_3_r1",
        "Condition1_timepoint_3_Sample_3_r2",
        "Condition1_timepoint_3_Sample_3_r3",
        "Condition1_timepoint_4_Sample_4_r1",
        "Condition1_timepoint_4_Sample_4_r2",
        "Condition1_timepoint_4_Sample_4_r3",
        "Condition1_timepoint_5_Sample_5_r1",
        "Condition1_timepoint_5_Sample_5_r2",
        "Condition1_timepoint_5_Sample_5_r3",
        "Condition2_timepoint_1_Sample_1_r1",
        "Condition2_timepoint_1_Sample_1_r2",
        "Condition2_timepoint_1_Sample_1_r3",
        "Condition2_timepoint_2_Sample_2_r1",
        "Condition2_timepoint_2_Sample_2_r2",
        "Condition2_timepoint_2_Sample_2_r3",
        "Condition2_timepoint_3_Sample_3_r1",
        "Condition2_timepoint_3_Sample_3_r2",
        "Condition2_timepoint_3_Sample_3_r3",
        "Condition2_timepoint_4_Sample_4_r1",
        "Condition2_timepoint_4_Sample_4_r2",
        "Condition2_timepoint_4_Sample_4_r3",
        "Condition2_timepoint_5_Sample_5_r1",
        "Condition2_timepoint_5_Sample_5_r2",
        "Condition2_timepoint_5_Sample_5_r3"
      ],
      "rows": 1045,
      "table": true,
      "tojson": true
    },
    {
      "name": "data2",
      "title": "A small dataset with 50 proteins and 30 samples for the example usage of RolDE",
      "object": "data2",
      "file": "data2.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Condition1_timepoint_1_4fmol_r1",
        "Condition1_timepoint_1_4fmol_r2",
        "Condition1_timepoint_1_4fmol_r3",
        "Condition1_timepoint_2_4fmol_r1",
        "Condition1_timepoint_2_4fmol_r2",
        "Condition1_timepoint_2_4fmol_r3",
        "Condition1_timepoint_3_10fmol_r1",
        "Condition1_timepoint_3_10fmol_r2",
        "Condition1_timepoint_3_10fmol_r3",
        "Condition1_timepoint_4_25fmol_r1",
        "Condition1_timepoint_4_25fmol_r2",
        "Condition1_timepoint_4_25fmol_r3",
        "Condition1_timepoint_5_50fmol_r1",
        "Condition1_timepoint_5_50fmol_r2",
        "Condition1_timepoint_5_50fmol_r3",
        "Condition2_timepoint_1_25fmol_r1",
        "Condition2_timepoint_1_25fmol_r2",
        "Condition2_timepoint_1_25fmol_r3",
        "Condition2_timepoint_2_25fmol_r1",
        "Condition2_timepoint_2_25fmol_r2",
        "Condition2_timepoint_2_25fmol_r3",
        "Condition2_timepoint_3_10fmol_r1",
        "Condition2_timepoint_3_10fmol_r2",
        "Condition2_timepoint_3_10fmol_r3",
        "Condition2_timepoint_4_4fmol_r1",
        "Condition2_timepoint_4_4fmol_r2",
        "Condition2_timepoint_4_4fmol_r3",
        "Condition2_timepoint_5_2fmol_r1",
        "Condition2_timepoint_5_2fmol_r2",
        "Condition2_timepoint_5_2fmol_r3"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
    },
    {
      "name": "data3",
      "title": "A semi-simulated UPS1 spike-in dataset with differences in longitudinal expression for the spike-in proteins - no missing values.",
      "object": "data3",
      "file": "data3.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Condition1_timepoint_1_4fmol_r1",
        "Condition1_timepoint_1_4fmol_r2",
        "Condition1_timepoint_1_4fmol_r3",
        "Condition1_timepoint_2_4fmol_r1",
        "Condition1_timepoint_2_4fmol_r2",
        "Condition1_timepoint_2_4fmol_r3",
        "Condition1_timepoint_3_10fmol_r1",
        "Condition1_timepoint_3_10fmol_r2",
        "Condition1_timepoint_3_10fmol_r3",
        "Condition1_timepoint_4_25fmol_r1",
        "Condition1_timepoint_4_25fmol_r2",
        "Condition1_timepoint_4_25fmol_r3",
        "Condition1_timepoint_5_50fmol_r1",
        "Condition1_timepoint_5_50fmol_r2",
        "Condition1_timepoint_5_50fmol_r3",
        "Condition2_timepoint_1_25fmol_r1",
        "Condition2_timepoint_1_25fmol_r2",
        "Condition2_timepoint_1_25fmol_r3",
        "Condition2_timepoint_2_25fmol_r1",
        "Condition2_timepoint_2_25fmol_r2",
        "Condition2_timepoint_2_25fmol_r3",
        "Condition2_timepoint_3_10fmol_r1",
        "Condition2_timepoint_3_10fmol_r2",
        "Condition2_timepoint_3_10fmol_r3",
        "Condition2_timepoint_4_4fmol_r1",
        "Condition2_timepoint_4_4fmol_r2",
        "Condition2_timepoint_4_4fmol_r3",
        "Condition2_timepoint_5_2fmol_r1",
        "Condition2_timepoint_5_2fmol_r2",
        "Condition2_timepoint_5_2fmol_r3"
      ],
      "rows": 1033,
      "table": true,
      "tojson": true
    },
    {
      "name": "des_matrix1",
      "title": "A RolDE design matrix for data1",
      "object": "des_matrix1",
      "file": "des_matrix1.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Sample Names",
        "Condition",
        "Time point",
        "Replicate/Individual"
      ],
      "rows": 30,
      "table": true,
      "tojson": true
    },
    {
      "name": "des_matrix2",
      "title": "A RolDE design matrix for data2",
      "object": "des_matrix2",
      "file": "des_matrix2.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Sample Names",
        "Condition",
        "Time point",
        "Replicate/Individual"
      ],
      "rows": 30,
      "table": true,
      "tojson": true
    },
    {
      "name": "des_matrix3",
      "title": "A RolDE design matrix for data3",
      "object": "des_matrix3",
      "file": "des_matrix3.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Sample Names",
        "Condition",
        "Time point",
        "Replicate/Individual"
      ],
      "rows": 30,
      "table": true,
      "tojson": true
    },
    {
      "name": "res1",
      "title": "RolDE results for data1",
      "object": "res1",
      "file": "res1.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "res3",
      "title": "RolDE results for data3",
      "object": "res3",
      "file": "res3.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "data1",
      "title": "A proteomics dataset with random protein expression values - no missing values.",
      "topics": [
        "data1"
      ]
    },
    {
      "page": "data2",
      "title": "A small dataset with 50 proteins and 30 samples for the example usage of RolDE",
      "topics": [
        "data2"
      ]
    },
    {
      "page": "data3",
      "title": "A semi-simulated UPS1 spike-in dataset with differences in longitudinal expression for the spike-in proteins - no missing values.",
      "topics": [
        "data3"
      ]
    },
    {
      "page": "des_matrix1",
      "title": "A RolDE design matrix for data1",
      "topics": [
        "des_matrix1"
      ]
    },
    {
      "page": "des_matrix2",
      "title": "A RolDE design matrix for data2",
      "topics": [
        "des_matrix2"
      ]
    },
    {
      "page": "des_matrix3",
      "title": "A RolDE design matrix for data3",
      "topics": [
        "des_matrix3"
      ]
    },
    {
      "page": "plotFindings",
      "title": "Plot RolDE results",
      "topics": [
        "plotFindings"
      ]
    },
    {
      "page": "res1",
      "title": "RolDE results for data1",
      "topics": [
        "res1"
      ]
    },
    {
      "page": "res3",
      "title": "RolDE results for data3",
      "topics": [
        "res3"
      ]
    },
    {
      "page": "RolDE",
      "title": "Robust longitudinal Differential Expression",
      "topics": [
        "RolDE"
      ]
    },
    {
      "page": "RolDE_Main",
      "title": "Robust longitudinal Differential Expression",
      "topics": [
        "RolDE_Main"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/RolDE/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "boot",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "digest",
    "doParallel",
    "doRNG",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "iterators",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "lme4",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "minqa",
    "nlme",
    "nloptr",
    "plyr",
    "qvalue",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "reshape2",
    "rlang",
    "rngtools",
    "ROTS",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "Introduction.Rmd",
      "filename": "Introduction.html",
      "title": "Introduction to the Robust longitudinal Differential Expression (RolDE) method",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Applying RolDE in example datasets with aligned time points",
        "Semi-simulated spike-in dataset",
        "Applying RolDE in example data with non aligned time points",
        "Changing the settings for RolDE",
        "Preparation of data for RolDE",
        "References"
      ],
      "created": "2021-04-09 12:57:33",
      "modified": "2022-10-11 13:20:56",
      "commits": 8
    }
  ],
  "_score": 5,
  "_indexed": true,
  "_nocasepkg": "rolde",
  "_universes": [
    "bioc",
    "elolab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-04-30T15:40:56.000Z",
      "distro": "noble",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "c7c1cec8f8fbf935d4869756889812e5c49f7b0b54ac084e46681a1dad5c629c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-04-30T15:39:19.000Z",
      "distro": "noble",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "dde4a58e522fcb71a22e0145d3f7efe3eb102582eb45b4ba3883987d453ea0a3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-04-30T17:11:53.000Z",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "3d8dc067c3be462db25aac5d0705250485fd17f6ce8804c1c440c259564f9f2c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-04-30T17:12:23.000Z",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "78f28fd4a229df220983602754aba5db2cafd9ba963030934b9b0211af99d2db",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-04-30T15:40:32.000Z",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "3e3eaaf93334b003adbab2fa3534fffeca13bb01eb4174f0ff91e7a973f0642e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-04-30T15:42:15.000Z",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "ea785e0caf7ff629b28594475487eacb3f5082cf05df692836d755ef13e86853",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-04-30T15:39:00.000Z",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "3b4390b3965f5d2d00462925797facd3470b94eae92928b909012aa4601d0211",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.17.0",
      "date": "2026-05-22T21:04:04.000Z",
      "commit": "6cb224542ca74a2c64c90d9966f54096c6a5a2a6",
      "fileid": "62fa3e46bd32333ef1751fe1b5c8e331d4ece8327de1ea311c9689684e63b22f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173747896"
    }
  ]
}