{
  "_id": "6a1ac7f31d7bb097a09dbe8c",
  "Package": "Maaslin2",
  "Title": "\"Multivariable Association Discovery in Population-scale\nMeta-omics Studies\"",
  "Year": "2021",
  "Version": "1.27.0",
  "Authors@R": "c(\nperson(\"Himel\", \"Mallick\", email = \"himel.stat.iitk@gmail.com\", role = \"aut\"),\nperson(\"Ali\", \"Rahnavard\", email = \"gholamali.rahnavard@gmail.com\", role = \"aut\"),\nperson(\"Thomas\", \"Kuntz\", email = \"tkuntz@hsph.harvard.edu\", role = \"aut\"),\nperson(\"Sagun\", \"Maharjan\", email = \"sagunmaharjann@gmail.com\", role = c(\"aut\", \"cre\"))\n)",
  "Description": "MaAsLin2 is comprehensive R package for efficiently\ndetermining multivariable association between clinical metadata\nand microbial meta'omic features. MaAsLin2 relies on general\nlinear models to accommodate most modern epidemiological study\ndesigns, including cross-sectional and longitudinal, and offers\na variety of data exploration, normalization, and\ntransformation methods. MaAsLin2 is the next generation of\nMaAsLin.",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "Collate": "fit.R utility_scripts.R viz.R Maaslin2.R",
  "URL": "http://huttenhower.sph.harvard.edu/maaslin2",
  "biocViews": "Metagenomics, Software, Microbiome, Normalization",
  "BugReports": "https://github.com/biobakery/maaslin2/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:35 UTC",
  "RemoteUrl": "https://github.com/bioc/Maaslin2",
  "RemoteRef": "HEAD",
  "RemoteSha": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:48:24 UTC",
    "User": "root"
  },
  "Author": "Himel Mallick [aut],\nAli Rahnavard [aut],\nThomas Kuntz [aut],\nSagun Maharjan [aut, cre]",
  "Maintainer": "Sagun Maharjan <sagunmaharjann@gmail.com>",
  "MD5sum": "5b0cfe955878f4c16c7a79a04ffde0e9",
  "_user": "bioc",
  "_type": "src",
  "_file": "Maaslin2_1.27.0.tar.gz",
  "_fileid": "19303e2d8042e30501ed32041cc73de9ac59a08d02bfb83612de3b02faa9ae2a",
  "_filesize": 451539,
  "_sha256": "19303e2d8042e30501ed32041cc73de9ac59a08d02bfb83612de3b02faa9ae2a",
  "_created": "2026-05-30T07:48:24.000Z",
  "_published": "2026-05-30T11:20:19.475Z",
  "_jobs": [
    {
      "job": 78634552466,
      "time": 180,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306612123"
    },
    {
      "job": 78634552472,
      "time": 334,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306627268"
    },
    {
      "job": 78634552461,
      "time": 279,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306622047"
    },
    {
      "job": 78634552474,
      "time": 153,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307795923"
    },
    {
      "job": 78634552470,
      "time": 150,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307794042"
    },
    {
      "job": 78634303422,
      "time": 320,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306594648"
    },
    {
      "job": 78634552462,
      "time": 162,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306610474"
    },
    {
      "job": 78634552482,
      "time": 214,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306615642"
    },
    {
      "job": 78634552481,
      "time": 208,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306615042"
    },
    {
      "job": 78634552484,
      "time": 220,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306616196"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Maaslin2",
  "_commit": {
    "id": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
    "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": 1777380635
  },
  "_maintainer": {
    "name": "Sagun Maharjan",
    "email": "sagunmaharjann@gmail.com",
    "login": "sagun98",
    "description": "",
    "uuid": 15079734
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "robustbase",
      "role": "Imports"
    },
    {
      "package": "biglm",
      "role": "Imports"
    },
    {
      "package": "pcaPP",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "metagenomeSeq",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "car",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "chemometrics",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "logging",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "lmerTest",
      "role": "Imports"
    },
    {
      "package": "hash",
      "role": "Imports"
    },
    {
      "package": "optparse",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "glmmTMB",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "cplm",
      "role": "Imports"
    },
    {
      "package": "pscl",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "metagenomics",
    "software",
    "microbiome",
    "normalization",
    "biobakery",
    "bioconductor",
    "differential-abundance-analysis",
    "false-discovery-rate",
    "multiple-covariates",
    "public",
    "r-tools",
    "repeated-measures",
    "tools"
  ],
  "_stars": 155,
  "_contributors": [
    {
      "user": "ljmciver",
      "count": 289,
      "uuid": 18152225
    },
    {
      "user": "tkuntz-hsph",
      "count": 45,
      "uuid": 73124413
    },
    {
      "user": "grahnavard",
      "count": 35,
      "uuid": 12532403
    },
    {
      "user": "himelmallick",
      "count": 19,
      "uuid": 18686976
    },
    {
      "user": "nturaga",
      "count": 12,
      "uuid": 2746443
    },
    {
      "user": "sagun98",
      "count": 12,
      "uuid": 15079734
    },
    {
      "user": "jwokaty",
      "count": 4,
      "uuid": 1744257
    },
    {
      "user": "andrewghazi",
      "count": 3,
      "uuid": 6763470
    },
    {
      "user": "nearinj",
      "count": 2,
      "uuid": 31660222
    },
    {
      "user": "willnickols",
      "count": 2,
      "uuid": 78048944
    },
    {
      "user": "kescobo",
      "count": 1,
      "uuid": 3502975
    },
    {
      "user": "zhangycbnu",
      "count": 1,
      "uuid": 5424360
    },
    {
      "user": "chuttenh",
      "count": 1,
      "uuid": 3082440
    },
    {
      "user": "kelsthom13",
      "count": 1,
      "uuid": 58088886
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1688,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Maaslin2"
  },
  "_mentions": 8,
  "_devurl": "https://github.com/biobakery/maaslin2",
  "_searchresults": 764,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/Maaslin2.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/biobakery/maaslin2",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "Maaslin2"
  ],
  "_help": [
    {
      "page": "Maaslin2",
      "title": "MaAsLin2 is the next generation of MaAsLin, a multivariable statistical framework for finding associations between clinical metadata and potentially high-dimensional microbial multi-omics data.",
      "topics": [
        "Maaslin2"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Maaslin2/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "biglm",
    "Biobase",
    "BiocGenerics",
    "bitops",
    "boot",
    "broom",
    "car",
    "carData",
    "caTools",
    "chemometrics",
    "class",
    "cli",
    "cluster",
    "coda",
    "codetools",
    "colorspace",
    "cowplot",
    "cplm",
    "cpp11",
    "data.table",
    "DBI",
    "DEoptimR",
    "Deriv",
    "doBy",
    "dplyr",
    "e1071",
    "edgeR",
    "farver",
    "foreach",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggplot2",
    "glmmTMB",
    "glmnet",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "hash",
    "isoband",
    "iterators",
    "KernSmooth",
    "labeling",
    "lars",
    "lattice",
    "lifecycle",
    "limma",
    "lme4",
    "lmerTest",
    "lmtest",
    "locfit",
    "logging",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "matrixStats",
    "mclust",
    "metagenomeSeq",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "optparse",
    "pbapply",
    "pbkrtest",
    "pcaPP",
    "permute",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "pls",
    "plyr",
    "proxy",
    "pscl",
    "purrr",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "reshape2",
    "rlang",
    "robustbase",
    "rpart",
    "S7",
    "sandwich",
    "scales",
    "shape",
    "som",
    "SparseM",
    "statmod",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "TMB",
    "tweedie",
    "urca",
    "utf8",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "Wrench",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "maaslin2.Rmd",
      "filename": "maaslin2.html",
      "title": "Maaslin2",
      "author": "Himel Mallick, Ali Rahnavard, Lauren McIver",
      "engine": "knitr::rmarkdown",
      "headings": [
        "MaAsLin2 User Manual",
        "Contents",
        "Description",
        "Requirements",
        "Installation",
        "From command line",
        "From R",
        "How to Run",
        "Input Files",
        "Output Files",
        "Run a Demo",
        "Command line",
        "In R",
        "Session Info",
        "Options",
        "Troubleshooting"
      ],
      "created": "2019-05-10 19:51:15",
      "modified": "2023-06-07 16:16:30",
      "commits": 28
    }
  ],
  "_score": 11.272073347773723,
  "_indexed": true,
  "_nocasepkg": "maaslin2",
  "_universes": [
    "bioc",
    "sagun98",
    "biobakery"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T07:52:12.000Z",
      "distro": "noble",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "085eb6681bade6115f80561ad27b95d014771ae04a697ebc2fba4b0f3b645abf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T07:51:23.000Z",
      "distro": "noble",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "8406df7e899ac78597bd3c5e45b7fa865c445c29221bb76b2e8bd71c3b484dc3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T11:17:25.000Z",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "3f4d5e6f8c4eb0152228fcb64e261a7000e562e83fb9043d462d91e354cee380",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T11:17:00.000Z",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "4a0f00a5d62ab9acb685a78e73d86ab169276a3a8a4aef3c7ab76ba886c3d703",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-05-30T07:51:22.000Z",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "eee8554c738043a18fd4ea418d10542c90583f662f2c1d38b5be06a11216c16e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T07:49:52.000Z",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "f6996bce14f51201973384cacfa882e522b9d54374e3741e7e88eb6a9402c289",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T07:49:48.000Z",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "35dd2f32a0a47126e58d2919271956f7188810386e2d98196ac9d286fa20f776",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T07:49:47.000Z",
      "commit": "6335054294def8c9e53cafcf1e8ddad00f24a94f",
      "fileid": "26f963be860e7e31a973afb7b079a6df2e4348fd548291f4e81a6018b24c54f6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678366454"
    }
  ]
}