{
  "_id": "6a19692aacfb0bcc41de8e92",
  "Package": "BLMA",
  "Date": "2020-06-22",
  "Type": "Package",
  "Title": "BLMA: A package for bi-level meta-analysis",
  "Version": "1.37.0",
  "Author": "Tin Nguyen <tinn@auburn.edu>, Hung Nguyen\n<pzb00047@auburn.edu>, and Sorin Draghici <sorin@wayne.edu>",
  "Maintainer": "Van-Dung Pham <dvp0001@auburn.edu>",
  "Description": "Suit of tools for bi-level meta-analysis. The package can\nbe used in a wide range of applications, including general\nhypothesis testings, differential expression analysis,\nfunctional analysis, and pathway analysis.",
  "biocViews": "GeneSetEnrichment, Pathways, DifferentialExpression,\nMicroarray",
  "License": "GPL (>=2)",
  "RoxygenNote": "7.3.1",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "make libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:45:35 UTC",
  "RemoteUrl": "https://github.com/bioc/BLMA",
  "RemoteRef": "HEAD",
  "RemoteSha": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
  "Packaged": {
    "Date": "2026-05-29 08:34:03 UTC",
    "User": "root"
  },
  "MD5sum": "b49ee56212071954f35e4228bb48115d",
  "_user": "bioc",
  "_type": "src",
  "_file": "BLMA_1.37.0.tar.gz",
  "_fileid": "338346d919a9d147baac61d2d2b28ce7a0beb21b228278b96546e1abe01bb33d",
  "_filesize": 2955320,
  "_sha256": "338346d919a9d147baac61d2d2b28ce7a0beb21b228278b96546e1abe01bb33d",
  "_created": "2026-05-29T08:34:03.000Z",
  "_published": "2026-05-29T10:23:38.177Z",
  "_jobs": [
    {
      "job": 78466466024,
      "time": 220,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7286599953"
    },
    {
      "job": 78466465998,
      "time": 520,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286687752"
    },
    {
      "job": 78466466018,
      "time": 487,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286678006"
    },
    {
      "job": 78466465991,
      "time": 239,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7288462089"
    },
    {
      "job": 78466466019,
      "time": 303,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7288484048"
    },
    {
      "job": 78465319859,
      "time": 466,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286534586"
    },
    {
      "job": 78466466010,
      "time": 184,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7286590416"
    },
    {
      "job": 78466466053,
      "time": 420,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7286657483"
    },
    {
      "job": 78466466003,
      "time": 456,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7286668299"
    },
    {
      "job": 78466466025,
      "time": 451,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7286665477"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BLMA",
  "_commit": {
    "id": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
    "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": 1777380335
  },
  "_maintainer": {
    "name": "Van-Dung Pham",
    "email": "dvp0001@auburn.edu",
    "login": "csieuluoi",
    "description": "",
    "uuid": 39341396
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "ROntoTools",
      "role": "Depends"
    },
    {
      "package": "GSA",
      "role": "Depends"
    },
    {
      "package": "PADOG",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "graph",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "parallel",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "metafor",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "BiocGenerics",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.36.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genesetenrichment",
    "pathways",
    "differentialexpression",
    "microarray"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 408,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BLMA"
  },
  "_mentions": 1,
  "_searchresults": 51,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BLMA.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addCLT",
    "bilevelAnalysisClassic",
    "bilevelAnalysisGene",
    "bilevelAnalysisGeneset",
    "bilevelAnalysisPathway",
    "fisherMethod",
    "getStatistics",
    "intraAnalysisClassic",
    "intraAnalysisGene",
    "loadKEGGPathways",
    "pORACalc",
    "stoufferMethod"
  ],
  "_datasets": [
    {
      "name": "data_GSE17054",
      "title": "Gene expression dataset GSE17054 from Majeti et al.",
      "object": "GSE17054",
      "file": "GSE17054.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "GSM426413",
        "GSM426414",
        "GSM426415",
        "GSM426416",
        "GSM426404",
        "GSM426405",
        "GSM426406",
        "GSM426407",
        "GSM426412"
      ],
      "rows": 4738,
      "table": true,
      "tojson": true
    },
    {
      "name": "data_GSE33223",
      "title": "Gene expression dataset GSE33223 from Bacher et al.",
      "object": "GSE33223",
      "file": "GSE33223.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "GSM822463",
        "GSM822464",
        "GSM822465",
        "GSM822466",
        "GSM822467",
        "GSM822468",
        "GSM822469",
        "GSM822470",
        "GSM822471",
        "GSM822472",
        "GSM822473",
        "GSM822474",
        "GSM822475",
        "GSM822476",
        "GSM822477",
        "GSM822478",
        "GSM822479",
        "GSM822480",
        "GSM822481",
        "GSM822482",
        "GSM822483",
        "GSM822484",
        "GSM822485",
        "GSM822486",
        "GSM822487",
        "GSM822488",
        "GSM822489",
        "GSM822490",
        "GSM822491",
        "GSM822492"
      ],
      "rows": 4114,
      "table": true,
      "tojson": true
    },
    {
      "name": "data_GSE42140",
      "title": "The gene expression dataset GSE42140 obtained from Gene Expression Omnibus",
      "object": "GSE42140",
      "file": "GSE42140.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "GSM1033424",
        "GSM1033426",
        "GSM1033438",
        "GSM1033450",
        "GSM1033452",
        "GSM1033427",
        "GSM1033428",
        "GSM1033429",
        "GSM1033430",
        "GSM1033431",
        "GSM1033432",
        "GSM1033433",
        "GSM1033434",
        "GSM1033435",
        "GSM1033436",
        "GSM1033437",
        "GSM1033439",
        "GSM1033440",
        "GSM1033444",
        "GSM1033445",
        "GSM1033446",
        "GSM1033448",
        "GSM1033449",
        "GSM1033454",
        "GSM1033456",
        "GSM1033458",
        "GSM1033459",
        "GSM1033460",
        "GSM1033461",
        "GSM1033462",
        "GSM1033463"
      ],
      "rows": 4114,
      "table": true,
      "tojson": true
    },
    {
      "name": "data_GSE57194",
      "title": "Gene expression dataset GSE57194 from Abdul-Nabi et al.",
      "object": "GSE57194",
      "file": "GSE57194.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "GSM1376943",
        "GSM1376944",
        "GSM1376945",
        "GSM1376946",
        "GSM1376947",
        "GSM1376948",
        "GSM1376955",
        "GSM1376956",
        "GSM1376957",
        "GSM1376958",
        "GSM1376959",
        "GSM1376960"
      ],
      "rows": 4114,
      "table": true,
      "tojson": true
    },
    {
      "name": "group_GSE17054",
      "title": "Gene expression dataset GSE17054 from Majeti et al.",
      "object": "GSE17054",
      "file": "GSE17054.RData",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "group_GSE33223",
      "title": "Gene expression dataset GSE33223 from Bacher et al.",
      "object": "GSE33223",
      "file": "GSE33223.RData",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "group_GSE42140",
      "title": "The gene expression dataset GSE42140 obtained from Gene Expression Omnibus",
      "object": "GSE42140",
      "file": "GSE42140.RData",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "group_GSE57194",
      "title": "Gene expression dataset GSE57194 from Abdul-Nabi et al.",
      "object": "GSE57194",
      "file": "GSE57194.RData",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addCLT",
      "title": "The additive method for meta-analysis",
      "topics": [
        "addCLT"
      ]
    },
    {
      "page": "bilevelAnalysisClassic",
      "title": "Bi-level meta-analysis in conjunction with a classical hypothesis testing method",
      "topics": [
        "bilevelAnalysisClassic"
      ]
    },
    {
      "page": "bilevelAnalysisGene",
      "title": "Bi-level meta-analysis of multiple expression datasets at the gene-level",
      "topics": [
        "bilevelAnalysisGene"
      ]
    },
    {
      "page": "bilevelAnalysisGeneset",
      "title": "Bi-level meta-analysis - applied to geneset enrichment analysis",
      "topics": [
        "bilevelAnalysisGeneset"
      ]
    },
    {
      "page": "bilevelAnalysisPathway",
      "title": "Bi-level meta-analysis - applied to pathway analysis",
      "topics": [
        "bilevelAnalysisPathway"
      ]
    },
    {
      "page": "fisherMethod",
      "title": "Fisher's method for meta-analysis",
      "topics": [
        "fisherMethod"
      ]
    },
    {
      "page": "getStatistics",
      "title": "Intergrative genes statistic",
      "topics": [
        "getStatistics"
      ]
    },
    {
      "page": "GSE17054",
      "title": "Gene expression dataset GSE17054 from Majeti et al.",
      "topics": [
        "data_GSE17054",
        "group_GSE17054",
        "GSE17054"
      ]
    },
    {
      "page": "GSE33223",
      "title": "Gene expression dataset GSE33223 from Bacher et al.",
      "topics": [
        "data_GSE33223",
        "group_GSE33223",
        "GSE33223"
      ]
    },
    {
      "page": "GSE42140",
      "title": "The gene expression dataset GSE42140 obtained from Gene Expression Omnibus",
      "topics": [
        "data_GSE42140",
        "group_GSE42140",
        "GSE42140"
      ]
    },
    {
      "page": "GSE57194",
      "title": "Gene expression dataset GSE57194 from Abdul-Nabi et al.",
      "topics": [
        "data_GSE57194",
        "group_GSE57194",
        "GSE57194"
      ]
    },
    {
      "page": "intraAnalysisClassic",
      "title": "Intra-experiment analysis in conjunction with classical hypothesis tests",
      "topics": [
        "intraAnalysisClassic"
      ]
    },
    {
      "page": "intraAnalysisGene",
      "title": "Intra-experiment analysis of an expression dataset at the gene-level",
      "topics": [
        "intraAnalysisGene"
      ]
    },
    {
      "page": "loadKEGGPathways",
      "title": "Load KEGG pathways and names",
      "topics": [
        "loadKEGGPathways"
      ]
    },
    {
      "page": "pORACalc",
      "title": "Over-representation Analysis",
      "topics": [
        "pORACalc"
      ]
    },
    {
      "page": "stoufferMethod",
      "title": "Stouffer's method for meta-analysis",
      "topics": [
        "stoufferMethod"
      ]
    }
  ],
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "digest",
    "doRNG",
    "fastmap",
    "foreach",
    "generics",
    "glue",
    "graph",
    "GSA",
    "hgu133a.db",
    "hgu133plus2.db",
    "httr",
    "IRanges",
    "iterators",
    "jsonlite",
    "KEGGdzPathwaysGEO",
    "KEGGgraph",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "limma",
    "mathjaxr",
    "Matrix",
    "memoise",
    "metadat",
    "metafor",
    "mime",
    "nlme",
    "numDeriv",
    "openssl",
    "org.Hs.eg.db",
    "PADOG",
    "pbapply",
    "pkgconfig",
    "png",
    "R6",
    "RCurl",
    "Rgraphviz",
    "rlang",
    "rngtools",
    "ROntoTools",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "statmod",
    "sys",
    "vctrs",
    "XML",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "BLMA.Rnw",
      "filename": "BLMA.pdf",
      "title": "BLMA",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2017-01-17 02:33:25",
      "modified": "2020-06-24 17:42:38",
      "commits": 7
    }
  ],
  "_score": 4.008600171761918,
  "_indexed": true,
  "_nocasepkg": "blma",
  "_universes": [
    "bioc",
    "csieuluoi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-29T08:38:19.000Z",
      "distro": "noble",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "65674e8936915fcd2ef2b6e508629ace3aab56a01413e057e2ee36dfb322c237",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.37.0",
      "date": "2026-05-29T08:38:01.000Z",
      "distro": "noble",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "96bd3f288c051572086bf53bac840376276076609873023eb9b2eabefe74f942",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-29T10:19:33.000Z",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "5291b9a0a0ffcf938d9925bfb5e6d040c2ad5a54854dfe4ad24fb650f06d8dab",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.37.0",
      "date": "2026-05-29T10:20:08.000Z",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "bbb460c2c2e9770dd7633ef3bd0e54a2385964ea0913d116554b3b20367e8898",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.37.0",
      "date": "2026-05-29T08:37:44.000Z",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "6daa519829c19565f3fe7cc44a7a212fabc1fca985289f50657c3e435347489d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-29T08:36:27.000Z",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "c716445ad10d9299efe3528b9e4a90102296b516c596721b5e03b8c2bcf756f6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-29T08:37:04.000Z",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "ca438a014e33a76b6fa23c8a444a9fb94c436185d9cb15fc9a968652ae219b3b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.37.0",
      "date": "2026-05-29T08:36:37.000Z",
      "commit": "72ed5fbdca7709fec3f68ef76d58707e8816a652",
      "fileid": "c7eb8297e9f293ce6855f2fb7444b22f892709881acd32a300c55f7d4deebd1b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626754510"
    }
  ]
}