{
  "_id": "6a3ab43544e65c5976a89ea9",
  "Package": "ADAM",
  "Type": "Package",
  "Title": "ADAM: Activity and Diversity Analysis Module",
  "Version": "1.29.0",
  "Date": "2023-04-10",
  "Authors@R": "c(person(given = \"André Luiz\",\nfamily = \"Molan\",\nrole = \"aut\",\nemail = \"andre.molan@unesp.br\"),\nperson(given = \"Giordano Bruno\",\nfamily = \"Sanches Seco\",\nrole = \"ctb\"),\nperson(given = \"Agnes\",\nfamily = \"Takeda\",\nrole = \"ctb\"),\nperson(given = \"Jose\",\nfamily = \"Rybarczyk Filho\",\nrole = c(\"ctb\", \"cre\", \"ths\"),\nemail = \"jose.luiz@unesp.br\")\n)",
  "Maintainer": "Jose Luiz Rybarczyk Filho <jose.luiz@unesp.br>",
  "Description": "ADAM is a GSEA R package created to group a set of genes\nfrom comparative samples (control versus experiment) belonging\nto different species according to their respective functions\n(Gene Ontology and KEGG pathways as default) and show their\nsignificance by calculating p-values referring togene diversity\nand activity. Each group of genes is called GFAG (Group of\nFunctionally Associated Genes).",
  "SystemRequirements": "C++11",
  "Encoding": "UTF-8",
  "RoxygenNote": "6.1.0",
  "License": "GPL (>= 2)",
  "biocViews": "GeneSetEnrichment, Pathways, KEGG, GeneExpression,\nMicroarray",
  "VignetteBuilder": "knitr",
  "LazyLoad": "yes",
  "NeedsCompilation": "yes",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:11 UTC",
  "RemoteUrl": "https://github.com/bioc/ADAM",
  "RemoteRef": "HEAD",
  "RemoteSha": "8f824061211964c7cfefb051e52af9724b00b00c",
  "Packaged": {
    "Date": "2026-06-23 16:06:12 UTC",
    "User": "root"
  },
  "Author": "André Luiz Molan [aut],\nGiordano Bruno Sanches Seco [ctb],\nAgnes Takeda [ctb],\nJose Rybarczyk Filho [ctb, cre, ths]",
  "MD5sum": "d39285810b5342a8b068624752a73e04",
  "_user": "bioc",
  "_type": "src",
  "_file": "ADAM_1.29.0.tar.gz",
  "_fileid": "9859fb22d1769b427a00e5947a97bbf223987d339549aca3c26f76362f44f559",
  "_filesize": 150478,
  "_sha256": "9859fb22d1769b427a00e5947a97bbf223987d339549aca3c26f76362f44f559",
  "_created": "2026-06-23T16:06:12.000Z",
  "_published": "2026-06-23T16:28:37.940Z",
  "_jobs": [
    {
      "job": 83001635223,
      "time": 194,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7826512028"
    },
    {
      "job": 83001635325,
      "time": 268,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7826543143"
    },
    {
      "job": 83001635352,
      "time": 325,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7826566426"
    },
    {
      "job": 83001635398,
      "time": 271,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7826544542"
    },
    {
      "job": 83001635310,
      "time": 323,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7826565458"
    },
    {
      "job": 83001635319,
      "time": 205,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7826856532"
    },
    {
      "job": 83001635277,
      "time": 413,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7826927937"
    },
    {
      "job": 83001635354,
      "time": 188,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7826858478"
    },
    {
      "job": 83001635316,
      "time": 483,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7826964487"
    },
    {
      "job": 83000594603,
      "time": 278,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7826427161"
    },
    {
      "job": 83001635351,
      "time": 287,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7826545662"
    },
    {
      "job": 83001635254,
      "time": 467,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7826625977"
    },
    {
      "job": 83001635357,
      "time": 478,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7826629639"
    },
    {
      "job": 83001635220,
      "time": 413,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7826601688"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/ADAM",
  "_commit": {
    "id": "8f824061211964c7cfefb051e52af9724b00b00c",
    "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": 1777380551
  },
  "_maintainer": {
    "name": "Jose Luiz Rybarczyk Filho",
    "email": "jose.luiz@unesp.br",
    "login": "jrybarczyk",
    "description": "",
    "uuid": 13757354
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.18",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "version": ">= 3.6.0",
      "role": "Imports"
    },
    {
      "package": "KEGGREST",
      "version": ">= 1.20.2",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "version": ">= 1.3-4",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 0.7.6",
      "role": "Imports"
    },
    {
      "package": "DT",
      "version": ">= 0.4",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "version": ">= 1.3.1",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.10.1",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genesetenrichment",
    "pathways",
    "kegg",
    "geneexpression",
    "microarray",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 441,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 482,
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/ADAM.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": [
    "ADAnalysis",
    "GFAGAnalysis"
  ],
  "_datasets": [
    {
      "name": "ExpressionAedes",
      "title": "Aedes aegypti RNA-seq data expression",
      "object": "ExpressionAedes",
      "file": "ExpressionAedes.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "control1",
        "experiment1",
        "control2",
        "experiment2"
      ],
      "rows": 34,
      "table": true,
      "tojson": true
    },
    {
      "name": "KeggPathwaysAedes",
      "title": "Relation between Aedes aegypti genes and KEGG pathways as ADAM input",
      "object": "KeggPathwaysAedes",
      "file": "KeggPathwaysAedes.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "pathwayID",
        "pathwayDescription"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ADAnalysis",
      "title": "Group of Functionally Associated Genes (GFAG) partial analysis",
      "topics": [
        "ADAnalysis"
      ]
    },
    {
      "page": "ExpressionAedes",
      "title": "Aedes aegypti RNA-seq data expression",
      "topics": [
        "ExpressionAedes"
      ]
    },
    {
      "page": "GFAGAnalysis",
      "title": "Group of Functionally Associated Genes (GFAG) complete analysis",
      "topics": [
        "GFAGAnalysis"
      ]
    },
    {
      "page": "KeggPathwaysAedes",
      "title": "Relation between Aedes aegypti genes and KEGG pathways as ADAM input",
      "topics": [
        "KeggPathwaysAedes"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "DBI",
    "DelayedArray",
    "digest",
    "dplyr",
    "DT",
    "evaluate",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "GenomicRanges",
    "glue",
    "GO.db",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "IRanges",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "otel",
    "pbapply",
    "pillar",
    "pkgconfig",
    "png",
    "promises",
    "R6",
    "rappdirs",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "sass",
    "Seqinfo",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "withr",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "ADAM.Rmd",
      "filename": "ADAM.html",
      "title": "ADAM: Activity and Diversity Analysis Module",
      "author": "André L. Molan, Giordano B. S. Seco, Agnes A. S. Takeda, Jose L. Rybarczyk-Filho",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "GFAGAnalysis",
        "ADAnalysis",
        "Session information",
        "References"
      ],
      "created": "2018-10-05 13:53:09",
      "modified": "2021-09-01 20:42:03",
      "commits": 8
    }
  ],
  "_score": 4.892094602690481,
  "_indexed": true,
  "_nocasepkg": "adam",
  "_universes": [
    "bioc",
    "jrybarczyk"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-06-23T16:09:27.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "1635dd519e181452c1a172544cd2f6782afce02916d5ee4707d3f61ddc6375d8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-06-23T16:09:41.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "170889670b71e2d7ffa5bfe962e733d655ca6b8381f01500e981824506a159d9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-06-23T16:09:31.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "69fd007e6ea3582a4835d0e7cc46478f6ac9e8cbb799cd1551a3e1c6112e5323",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-06-23T16:09:42.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "a49504a20ea92506b33cc6d76faefd885b67b3863f24b05dbc9878435ba2c1a9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-06-23T16:22:16.000Z",
      "arch": "aarch64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "325b370468e9329bc1b753521df8dc944cc068d4478b0e139102d51d1ef45921",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-06-23T16:23:00.000Z",
      "arch": "x86_64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "3a1f55a8d2e1cca83a0458d1f22de475a3436e12eda596dd98990978563c20c3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-06-23T16:22:26.000Z",
      "arch": "aarch64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "9009c4d455545bdbb98f10902730c906b0e0c6d7699b26208ebfe1b56cbb8bc2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-06-23T16:24:14.000Z",
      "arch": "x86_64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "05e7429c408bc19358610ee41b5fd2e75c59834ab92f2c614c5dbcc76ff9fa56",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.29.0",
      "date": "2026-06-23T16:11:21.000Z",
      "arch": "emscripten",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "eadb0d58d27abd93e49ad56707cc9ab5619eaaa52b19fb737ae3270fbc6c9b87",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-06-23T16:11:46.000Z",
      "arch": "x86_64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "dd13325c964cd770f0749a5cf8ac5dacdb35f520e06911f86f749ead078ef730",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-06-23T16:12:11.000Z",
      "arch": "x86_64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "5c222a5af4ca6f84c445a2ae38c6a8b5879660e521fdd74a4dd0d4b4d041aed5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-06-23T16:11:07.000Z",
      "arch": "x86_64",
      "commit": "8f824061211964c7cfefb051e52af9724b00b00c",
      "fileid": "a871fd0da34837d52bf6af2c44a75a3bbf50e3aafe2b0ee172ce65a83704f100",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28039141022"
    }
  ]
}