{
  "_id": "6abe600e99f7aa8c6aa56029",
  "Package": "zenith",
  "Type": "Package",
  "Title": "Gene set analysis following differential expression using linear\n(mixed) modeling with dream",
  "Version": "1.15.0",
  "Date": "2025-04-03",
  "Authors@R": "person(\"Gabriel\", \"Hoffman\", role=c(\"aut\", \"cre\"), email=\"gabriel.hoffman@mssm.edu\", comment=c(ORCID=\"0000-0002-0957-0224\"))",
  "Description": "Zenith performs gene set analysis on the result of\ndifferential expression using linear (mixed) modeling with\ndream by considering the correlation between gene expression\ntraits.  This package implements the camera method from the\nlimma package proposed by Wu and Smyth (2012).  Zenith is a\nsimple extension of camera to be compatible with linear mixed\nmodels implemented in variancePartition::dream().",
  "VignetteBuilder": "knitr",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "URL": "https://DiseaseNeuroGenomics.github.io/zenith",
  "BugReports": "https://github.com/DiseaseNeuroGenomics/zenith/issues",
  "biocViews": "RNASeq, GeneExpression, GeneSetEnrichment,\nDifferentialExpression, BatchEffect, QualityControl,\nRegression, Epigenetics, FunctionalGenomics, Transcriptomics,\nNormalization, Preprocessing, Microarray, ImmunoOncology,\nSoftware",
  "RdMacros": "Rdpack",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libxml2-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:49 UTC",
  "RemoteUrl": "https://github.com/bioc/zenith",
  "RemoteRef": "HEAD",
  "RemoteSha": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-01 12:41:03 UTC",
    "User": "root"
  },
  "Author": "Gabriel Hoffman [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-0957-0224>)",
  "Maintainer": "Gabriel Hoffman <gabriel.hoffman@mssm.edu>",
  "_user": "bioc",
  "_type": "src",
  "_file": "zenith_1.15.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/71dfd22b94fcfbf7089c8d452fc8dceff6e722fea8e4a0ab5379c8807c5adb8e",
  "_filesize": 218301,
  "_sha256": "71dfd22b94fcfbf7089c8d452fc8dceff6e722fea8e4a0ab5379c8807c5adb8e",
  "_expires": "2027-01-09T13:28:44.000Z",
  "_created": "2026-10-01T12:41:03.000Z",
  "_published": "2026-10-01T13:28:46.086Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661",
  "_status": "success",
  "_upstream": "https://github.com/bioc/zenith",
  "_commit": {
    "id": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
    "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": 1777381129
  },
  "_maintainer": {
    "name": "Gabriel Hoffman",
    "email": "gabriel.hoffman@mssm.edu",
    "login": "gabrielhoffman",
    "orcid": "0000-0002-0957-0224",
    "description": "Statistical genomics",
    "uuid": 13241293
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 110373195162,
      "time": 247,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11162992801"
    },
    {
      "job": 110373194896,
      "time": 511,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11163038420"
    },
    {
      "job": 110373195091,
      "time": 516,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11162393647"
    },
    {
      "job": 110373195129,
      "time": 307,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11166745435"
    },
    {
      "job": 110373194903,
      "time": 371,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11165436941"
    },
    {
      "job": 110370696589,
      "time": 398,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11162057486"
    },
    {
      "job": 110373195086,
      "time": 238,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11162697948"
    },
    {
      "job": 110373195141,
      "time": 392,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11162728218"
    },
    {
      "job": 110373195080,
      "time": 309,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11163272480"
    },
    {
      "job": 110373195216,
      "time": 357,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11163252904"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "variancePartition",
      "version": ">= 1.26.0",
      "role": "Imports"
    },
    {
      "package": "EnrichmentBrowser",
      "version": ">= 2.22.0",
      "role": "Imports"
    },
    {
      "package": "GSEABase",
      "version": ">= 1.54.0",
      "role": "Imports"
    },
    {
      "package": "msigdbr",
      "role": "Imports"
    },
    {
      "package": "Rfast",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "progress",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Rdpack",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "pander",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "tweeDEseqCountData",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.15.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.14.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "rnaseq",
    "geneexpression",
    "genesetenrichment",
    "differentialexpression",
    "batcheffect",
    "qualitycontrol",
    "regression",
    "epigenetics",
    "functionalgenomics",
    "transcriptomics",
    "normalization",
    "preprocessing",
    "microarray",
    "immunooncology",
    "software"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "gehoffman",
      "count": 66,
      "uuid": 8697260
    },
    {
      "user": "gabrielhoffman",
      "count": 8,
      "uuid": 13241293
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    },
    {
      "user": "hoondy",
      "count": 2,
      "uuid": 6531609
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 471,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 628,
    "source": "https://www.bioconductor.org/packages/stats/bioc/zenith"
  },
  "_devurl": "https://github.com/diseaseneurogenomics/zenith",
  "_pkgdown": "https://DiseaseNeuroGenomics.github.io/zenith",
  "_searchresults": 218,
  "_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/zenith.html"
  ],
  "_homeurl": "https://github.com/diseaseneurogenomics/zenith",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "get_GeneOntology",
    "get_MSigDB",
    "plotZenithResults",
    "zenith",
    "zenith_gsa",
    "zenithPR_gsa"
  ],
  "_help": [
    {
      "page": "dot-rankSumTestWithCorrelation",
      "title": "Two Sample Wilcoxon-Mann-Whitney Rank Sum Test Allowing For Correlation",
      "topics": [
        ".rankSumTestWithCorrelation"
      ]
    },
    {
      "page": "corInGeneSet",
      "title": "Evaluate mean correlation between residuals in gene set",
      "topics": [
        "corInGeneSet"
      ]
    },
    {
      "page": "get_GeneOntology",
      "title": "Load Gene Ontology genesets",
      "topics": [
        "get_GeneOntology"
      ]
    },
    {
      "page": "get_MSigDB",
      "title": "Load MSigDB genesets",
      "topics": [
        "get_MSigDB"
      ]
    },
    {
      "page": "plotZenithResults",
      "title": "Heatmap of zenith results using ggplot2",
      "topics": [
        "plotZenithResults"
      ]
    },
    {
      "page": "zenith",
      "title": "Gene set analysis following differential expression with dream",
      "topics": [
        "zenith"
      ]
    },
    {
      "page": "zenith_gsa-methods",
      "title": "Perform gene set analysis using zenith",
      "topics": [
        "zenith_gsa",
        "zenith_gsa,MArrayLM,GeneSetCollection,ANY-method",
        "zenith_gsa,MArrayLM,GeneSetCollection-method"
      ]
    },
    {
      "page": "zenithPR_gsa",
      "title": "Gene set analysis using pre-computed test statistic",
      "topics": [
        "zenithPR_gsa"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/zenith/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "aod",
    "askpass",
    "assertthat",
    "babelgene",
    "backports",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "broom",
    "cachem",
    "caTools",
    "cli",
    "codetools",
    "colorspace",
    "corpcor",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "Deriv",
    "dir.expiry",
    "doBy",
    "dplyr",
    "edgeR",
    "EnrichmentBrowser",
    "EnvStats",
    "fANCOVA",
    "farver",
    "fastmap",
    "filelock",
    "forecast",
    "formatR",
    "fracdiff",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "GO.db",
    "gplots",
    "graph",
    "graphite",
    "GSEABase",
    "gtable",
    "gtools",
    "hms",
    "httr",
    "httr2",
    "hwriter",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGgraph",
    "KEGGREST",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "lme4",
    "lmerTest",
    "lmtest",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "minqa",
    "modelr",
    "msigdbr",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "nortest",
    "numDeriv",
    "openssl",
    "org.Hs.eg.db",
    "pathview",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppParallel",
    "RCurl",
    "Rdpack",
    "reformulas",
    "remaCor",
    "reshape2",
    "Rfast",
    "Rgraphviz",
    "RhpcBLASctl",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "safe",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SparseM",
    "SPIA",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "variancePartition",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "xtable",
    "XVector",
    "zigg",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "loading_genesets.Rmd",
      "filename": "loading_genesets.html",
      "title": "Loading gene sets",
      "author": "Gabriel Hoffman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Easy loading of gene set databases",
        "Other databases",
        "Custom gene sets",
        "Session Info"
      ],
      "created": "2022-05-13 19:11:21",
      "modified": "2025-03-19 17:30:19",
      "commits": 2
    },
    {
      "source": "zenith.Rmd",
      "filename": "zenith.html",
      "title": "Zenith gene set testing after dream analysis",
      "author": "Gabriel Hoffman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Standard workflow",
        "Session Info"
      ],
      "created": "2022-04-08 18:37:15",
      "modified": "2022-07-06 23:30:25",
      "commits": 8
    }
  ],
  "_score": 6.5937289987079115,
  "_indexed": true,
  "_nocasepkg": "zenith",
  "_universes": [
    "bioc",
    "gabrielhoffman",
    "diseaseneurogenomics"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-10-01T12:46:34.000Z",
      "distro": "resolute",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/bfa6698bd117eb76888ff79cdd1b07d5779f521c75eec97d79cde0b9d9fc8883",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-10-01T12:46:42.000Z",
      "distro": "resolute",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/a95c57119c6d81ec61b8380f123c10e2172dfeb145905955b3970996724265ba",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-10-01T13:23:48.000Z",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/76346d83cae5b58402e368f455940b4310fe081467614b54d1be278ce33bf0a9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-10-01T13:24:09.000Z",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/768ad2c18459265e1fcf4041cbe10a1316cd14c02830feb8d549b0b85aa10a88",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.15.0",
      "date": "2026-10-01T12:45:40.000Z",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/d3fc0161aee03ef8fdff97837607c42e01e9c6a0fe73f2217a03053e10dbe0fa",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-10-01T12:44:01.000Z",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/03f2139b3660c000c58d62b8de0dea9fef51718f4da39b127a8a175f77617bc5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-10-01T12:43:28.000Z",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/ee4324ba052104921df832c8978de8dff475b5f037c526a2c4ee89d7b5ea4e3f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-10-01T12:43:42.000Z",
      "commit": "a5f57fabb9cb1488e12c980b8fb3531f0549fbc3",
      "fileid": "https://r2.ropensci.org/3b515075f9fbded16be8cdc89f9506375bb2b93a89c9536629b6caaecb9cce14",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36862707661"
    }
  ]
}