{
  "_id": "6a17dff3acfb0bcc41d9e7d5",
  "Package": "dearseq",
  "Type": "Package",
  "Title": "Differential Expression Analysis for RNA-seq data through a\nrobust variance component test",
  "Version": "1.25.0",
  "Date": "2023-06-16",
  "Authors@R": "c(person(\"Denis\", \"Agniel\", role = c(\"aut\"),\nemail = \"denis.agniel@gmail.com\"),\nperson(\"Boris P.\", \"Hejblum\", role = c(\"aut\", \"cre\"),\nemail = \"boris.hejblum@u-bordeaux.fr\",\ncomment = c(ORCID=\"0000-0003-0646-452X\")),\nperson(\"Marine\", \"Gauthier\", role = c(\"aut\"),\nemail = \"marine.gauthier@u-bordeaux.fr\"),\nperson(\"Mélanie\", \"Huchon\", role = c(\"ctb\"),\nemail = \"melanie.huchon@u-bordeaux.fr\"))",
  "Description": "Differential Expression Analysis RNA-seq data with\nvariance component score test accounting for data\nheteroscedasticity through precision weights. Perform both\ngene-wise and gene set analyses, and can deal with repeated or\nlongitudinal data. Methods are detailed in: i) Agniel D &\nHejblum BP (2017) Variance component score test for time-course\ngene set analysis of longitudinal RNA-seq data, Biostatistics,\n18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R &\nHejblum BP (2020) dearseq: a variance component score test for\nRNA-Seq differential analysis that effectively controls the\nfalse discovery rate, NAR Genomics and Bioinformatics,\n2(4):lqaa093.",
  "License": "GPL-2 | file LICENSE",
  "biocViews": "BiomedicalInformatics, CellBiology, DifferentialExpression,\nDNASeq, GeneExpression, Genetics, GeneSetEnrichment,\nImmunoOncology, KEGG, Regression, RNASeq, Sequencing,\nSystemsBiology, TimeCourse, Transcription, Transcriptomics",
  "BugReports": "https://github.com/borishejblum/dearseq/issues",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:35 UTC",
  "RemoteUrl": "https://github.com/bioc/dearseq",
  "RemoteRef": "HEAD",
  "RemoteSha": "568dec0cec0237e4ea988f7d71763e607c16b487",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:20:46 UTC",
    "User": "root"
  },
  "Author": "Denis Agniel [aut],\nBoris P. Hejblum [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0646-452X>),\nMarine Gauthier [aut],\nMélanie Huchon [ctb]",
  "Maintainer": "Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>",
  "MD5sum": "8a80f08a9174e15733424ce1859b5ee9",
  "_user": "bioc",
  "_type": "src",
  "_file": "dearseq_1.25.0.tar.gz",
  "_fileid": "666f9292782011105650e6774fc57f4d41c13b859cf764314e016a7c4134980d",
  "_filesize": 1410906,
  "_sha256": "666f9292782011105650e6774fc57f4d41c13b859cf764314e016a7c4134980d",
  "_created": "2026-05-28T06:20:46.000Z",
  "_published": "2026-05-28T06:25:55.502Z",
  "_jobs": [
    {
      "job": 78235260854,
      "time": 210,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7259081389"
    },
    {
      "job": 78235260878,
      "time": 258,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259092321"
    },
    {
      "job": 78235260873,
      "time": 227,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259085422"
    },
    {
      "job": 78235260882,
      "time": 127,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259076268"
    },
    {
      "job": 78235260872,
      "time": 155,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259087534"
    },
    {
      "job": 78234305660,
      "time": 489,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259030294"
    },
    {
      "job": 78235260868,
      "time": 152,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259068411"
    },
    {
      "job": 78235260877,
      "time": 166,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259071331"
    },
    {
      "job": 78235260874,
      "time": 148,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259067534"
    },
    {
      "job": 78235260955,
      "time": 142,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259066342"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/dearseq",
  "_commit": {
    "id": "568dec0cec0237e4ea988f7d71763e607c16b487",
    "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": 1777380695
  },
  "_maintainer": {
    "name": "Boris P. Hejblum",
    "email": "boris.hejblum@u-bordeaux.fr",
    "login": "borishejblum",
    "description": "",
    "uuid": 5277851,
    "orcid": "0000-0003-0646-452X"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "CompQuadForm",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "KernSmooth",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scattermore",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "statmod",
      "role": "Imports"
    },
    {
      "package": "survey",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "viridisLite",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "BiocSet",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    },
    {
      "package": "DESeq2",
      "role": "Suggests"
    },
    {
      "package": "GEOquery",
      "role": "Suggests"
    },
    {
      "package": "GSA",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "readxl",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "S4Vectors",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.25.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.24.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "biomedicalinformatics",
    "cellbiology",
    "differentialexpression",
    "dnaseq",
    "geneexpression",
    "genetics",
    "genesetenrichment",
    "immunooncology",
    "kegg",
    "regression",
    "rnaseq",
    "sequencing",
    "systemsbiology",
    "timecourse",
    "transcription",
    "transcriptomics"
  ],
  "_stars": 8,
  "_contributors": [
    {
      "user": "borishejblum",
      "count": 346,
      "uuid": 5277851
    },
    {
      "user": "mgauth",
      "count": 30,
      "uuid": 37074876
    },
    {
      "user": "denisagniel",
      "count": 12,
      "uuid": 3752811
    },
    {
      "user": "nturaga",
      "count": 10,
      "uuid": 2746443
    },
    {
      "user": "melaniehuchon",
      "count": 6,
      "uuid": 82106417
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "larrouture",
      "count": 3,
      "uuid": 72789673
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 546,
    "source": "https://www.bioconductor.org/packages/stats/bioc/dearseq"
  },
  "_devurl": "https://github.com/borishejblum/dearseq",
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/dearseq.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/borishejblum/dearseq",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "dear_seq",
    "dgsa_seq",
    "permPvals",
    "plot_hist_pvals",
    "plot_ord_pvals",
    "plot_weights",
    "sp_weights",
    "spaghettiPlot1GS",
    "vc_score",
    "vc_score_h",
    "vc_score_h_perm",
    "vc_score_perm",
    "vc_test_asym",
    "vc_test_perm",
    "voom_weights"
  ],
  "_datasets": [
    {
      "name": "baduel_gmt",
      "title": "Small portion of RNA-seq data from plant physiology study.",
      "object": "baduel_5gs",
      "file": "baduel_5gs.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "design",
      "title": "Small portion of RNA-seq data from plant physiology study.",
      "object": "baduel_5gs",
      "file": "baduel_5gs.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "Intercept",
        "Population",
        "AgeWeeks",
        "Replicate",
        "Vernalized",
        "PopulationKA",
        "AgeWeeks_Population",
        "AgeWeeks_Vernalized",
        "Vernalized_Population",
        "AgeWeeks_Vernalized_Population"
      ],
      "rows": 48,
      "table": true,
      "tojson": true
    },
    {
      "name": "expr_norm_corr",
      "title": "Small portion of RNA-seq data from plant physiology study.",
      "object": "baduel_5gs",
      "file": "baduel_5gs.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "KA_3_1",
        "KA_3_2",
        "KA_3_3",
        "TBG_3_1",
        "TBG_3_2",
        "TBG_3_3",
        "KA_4_1",
        "KA_4_2",
        "KA_4_3",
        "TBG_4_1",
        "TBG_4_2",
        "TBG_4_3",
        "KA_5_1",
        "KA_5_2",
        "KA_5_3",
        "TBG_5_1",
        "TBG_5_2",
        "TBG_5_3",
        "KA_5_1V",
        "KA_5_2V",
        "KA_5_3V",
        "TBG_5_1V",
        "TBG_5_2V",
        "TBG_5_3V",
        "KA_9_1",
        "KA_9_2",
        "KA_9_3",
        "TBG_9_1",
        "TBG_9_2",
        "TBG_9_3",
        "KA_9_1V",
        "KA_9_2V",
        "KA_9_3V",
        "TBG_9_1V",
        "TBG_9_2V",
        "TBG_9_3V",
        "KA_13_1",
        "KA_13_2",
        "KA_13_3",
        "TBG_13_1",
        "TBG_13_2",
        "TBG_13_3",
        "KA_13_1V",
        "KA_13_2V",
        "KA_13_3V",
        "TBG_13_1V",
        "TBG_13_2V",
        "TBG_13_3V"
      ],
      "rows": 2454,
      "table": true,
      "tojson": true
    },
    {
      "name": "PBT_gmt",
      "title": "PBT gene sets related to kidney transplant",
      "object": "PBT_gmt",
      "file": "PBT_gmt.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dearseq-package",
      "title": "dearseq: Differential Expression Analysis for RNA-seq data through a robust variance component test",
      "topics": [
        "dearseq-package",
        "dearseq"
      ]
    },
    {
      "page": "baduel_5gs",
      "title": "Small portion of RNA-seq data from plant physiology study.",
      "topics": [
        "baduel",
        "baduel_5gs",
        "baduel_gmt",
        "design",
        "expr_norm_corr"
      ]
    },
    {
      "page": "dear_seq",
      "title": "Differential expression analyis of RNA-seq data through a variance component test",
      "topics": [
        "dear_seq"
      ]
    },
    {
      "page": "dgsa_seq",
      "title": "Time-course Gene Set Analysis",
      "topics": [
        "dgsa_seq"
      ]
    },
    {
      "page": "PBT_gmt",
      "title": "PBT gene sets related to kidney transplant",
      "topics": [
        "PBT",
        "PBT_gmt"
      ]
    },
    {
      "page": "permPvals",
      "title": "Exact permutation p-values",
      "topics": [
        "permPvals"
      ]
    },
    {
      "page": "plot_hist_pvals",
      "title": "Plotting raw p-values histogram",
      "topics": [
        "plot_hist_pvals"
      ]
    },
    {
      "page": "plot_ord_pvals",
      "title": "Plot of gene-wise p-values",
      "topics": [
        "plot_ord_pvals"
      ]
    },
    {
      "page": "plot_weights",
      "title": "Plotting mean-variance fit for precision weights estimation",
      "topics": [
        "plot_weights"
      ]
    },
    {
      "page": "plot.dearseq",
      "title": "Plot method for dearseq objects",
      "topics": [
        "plot.dearseq"
      ]
    },
    {
      "page": "sp_weights",
      "title": "Non parametric local heteroscedasticity weights",
      "topics": [
        "sp_weights"
      ]
    },
    {
      "page": "spaghettiPlot1GS",
      "title": "Spaghetti plot for Specific Gene Set",
      "topics": [
        "spaghettiPlot1GS"
      ]
    },
    {
      "page": "summary.dearseq",
      "title": "Summary method for dearseq objects",
      "topics": [
        "print.summary.dearseq",
        "summary.dearseq"
      ]
    },
    {
      "page": "vc_test_asym",
      "title": "Asymptotic variance component test statistic and p-value",
      "topics": [
        "vc_test_asym"
      ]
    },
    {
      "page": "vc_test_perm",
      "title": "Permutation-based variance component test statistic and p-value",
      "topics": [
        "vc_test_perm"
      ]
    },
    {
      "page": "voom_weights",
      "title": "Precision weights accounting for heteroscedasticity in RNA-seq count data",
      "topics": [
        "voom_weights"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/dearseq/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/bioc/dearseq/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "CompQuadForm",
    "cpp11",
    "DBI",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "KernSmooth",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "matrixStats",
    "minqa",
    "mitools",
    "numDeriv",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "scattermore",
    "statmod",
    "stringi",
    "stringr",
    "survey",
    "survival",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "dearseqUserguide.Rmd",
      "filename": "dearseqUserguide.html",
      "title": "User guide to the dearseq R package",
      "author": "Marine Gauthier, Denis Agniel, Boris Hejblum",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview of dearseq",
        "Using dearseq for a gene-wise analysis",
        "Getting started using dear_seq()",
        "An example analysis",
        "Data preparation",
        "Design data matrix",
        "Gene expression matrix",
        "Identifying differentially expressed genes (DEG) from dearseq variance component score test",
        "Using gene expression matrix of raw counts",
        "Using dearseq for gene-set analysis",
        "Bibliography",
        "Appendix",
        "GEOquery package",
        "readxl",
        "Session Info"
      ],
      "created": "2019-05-16 08:40:44",
      "modified": "2022-02-01 15:52:06",
      "commits": 22
    }
  ],
  "_score": 6.334453751150931,
  "_indexed": true,
  "_nocasepkg": "dearseq",
  "_universes": [
    "bioc",
    "borishejblum"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.25.0",
      "date": "2026-05-28T06:24:42.000Z",
      "distro": "noble",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "98c8df0acd641a051e94ec4de0e160c892ca58b9e2cadf7e56477faee98e287f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.25.0",
      "date": "2026-05-28T06:24:11.000Z",
      "distro": "noble",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "f5630e3ea0138785f923feeb6dc29dca86202cdc8be9f15faa6bda7260a9a8e7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.25.0",
      "date": "2026-05-28T06:23:51.000Z",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "df63f3618bb4b4e74444b6053939c18ad8a813c8f5113bc035c493c356135d64",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.25.0",
      "date": "2026-05-28T06:24:28.000Z",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "93c33fe4f637976850134cd6b914b481621bb4895e1a6619df399611645b4253",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.25.0",
      "date": "2026-05-28T06:23:53.000Z",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "d24581e583fa10daa505c101871fc1f0af08efb7ea098f8e49744f967ad32ab9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-05-28T06:22:58.000Z",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "4d320df7c1c93771a24b626f2dc105a58fc7dbd0dd6f6761661932cf7ce00e08",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-05-28T06:22:42.000Z",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "856d2de862670d7f25f64183f1ce9b5592e1bce6ead32a9121d11a320a2688a7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-05-28T06:22:39.000Z",
      "commit": "568dec0cec0237e4ea988f7d71763e607c16b487",
      "fileid": "ac0db591bca4f0cce651ab0eaf41eb04aab805e7c68ee57fc52191af803f5fd0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558091747"
    }
  ]
}