{
  "_id": "6a493f05a19c9318096e7e7f",
  "Package": "SDAMS",
  "Type": "Package",
  "Title": "Differential Abundant/Expression Analysis for Metabolomics,\nProteomics and single-cell RNA sequencing Data",
  "Version": "1.33.0",
  "Date": "2023-07-21",
  "Author": "Yuntong Li <liyuntong0704@gmail.com>, Chi Wang\n<chi.wang@uky.edu>, Li Chen <lichenuky@uky.edu>",
  "Maintainer": "Yuntong Li <liyuntong0704@gmail.com>",
  "Description": "This Package utilizes a Semi-parametric Differential\nAbundance/expression analysis (SDA) method for metabolomics and\nproteomics data from mass spectrometry as well as single-cell\nRNA sequencing data. SDA is able to robustly handle\nnon-normally distributed data and provides a clear\nquantification of the effect size.",
  "License": "GPL",
  "LazyLoad": "no",
  "NeedsCompilation": "no",
  "biocViews": "ImmunoOncology, DifferentialExpression, Metabolomics,\nProteomics, MassSpectrometry, SingleCell",
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:48 UTC",
  "RemoteUrl": "https://github.com/bioc/SDAMS",
  "RemoteRef": "HEAD",
  "RemoteSha": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
  "Packaged": {
    "Date": "2026-07-04 04:26:26 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "SDAMS_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/6688f6d978e3f168305ac049182bd037a0485a065086a2f0f55e47def8ee8c49",
  "_filesize": 1357495,
  "_sha256": "6688f6d978e3f168305ac049182bd037a0485a065086a2f0f55e47def8ee8c49",
  "_expires": "2026-10-12T17:12:36.000Z",
  "_created": "2026-07-04T04:26:26.000Z",
  "_published": "2026-07-04T17:12:37.617Z",
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964",
  "_status": "success",
  "_upstream": "https://github.com/bioc/SDAMS",
  "_commit": {
    "id": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
    "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": 1777380468
  },
  "_maintainer": {
    "name": "Yuntong Li",
    "email": "liyuntong0704@gmail.com",
    "login": "stat-li",
    "description": "",
    "uuid": 36005627
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85151155133,
      "time": 183,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8078301233"
    },
    {
      "job": 85151155138,
      "time": 306,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8078315290"
    },
    {
      "job": 85151155145,
      "time": 319,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8078316583"
    },
    {
      "job": 85151155135,
      "time": 176,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8078300424"
    },
    {
      "job": 85151155263,
      "time": 158,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8078298577"
    },
    {
      "job": 85151154965,
      "time": 236,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8078280605"
    },
    {
      "job": 85151155129,
      "time": 167,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8078299495"
    },
    {
      "job": 85151155158,
      "time": 249,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8078309034"
    },
    {
      "job": 85151155162,
      "time": 235,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8078307425"
    },
    {
      "job": 85151155241,
      "time": 236,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8078307557"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "trust",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "differentialexpression",
    "metabolomics",
    "proteomics",
    "massspectrometry",
    "singlecell"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 2,
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/SDAMS.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "createSEFromCSV",
    "createSEFromMatrix",
    "SDA"
  ],
  "_datasets": [
    {
      "name": "exampleSingleCell",
      "title": "Two example datasets for SDAMS package",
      "object": "exampleSingleCell",
      "file": "exampleSingleCell.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exampleSumExp",
      "title": "Two example datasets for SDAMS package",
      "object": "exampleSumExp",
      "file": "exampleSumExp.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "SDAMS-package",
      "title": "SDAMS package for differential abundance/expression analysis of Metabolomics, Proteomics and single-cell RNA sequencing data",
      "topics": [
        "SDAMS-package"
      ]
    },
    {
      "page": "dataInput",
      "title": "Mass spectrometry data input",
      "topics": [
        "createSEFromCSV",
        "createSEFromMatrix",
        "dataInput"
      ]
    },
    {
      "page": "exampleData",
      "title": "Two example datasets for SDAMS package",
      "topics": [
        "exampleData",
        "exampleSingleCell",
        "exampleSumExp"
      ]
    },
    {
      "page": "SDA",
      "title": "Semi-parametric differential abuandance/expression analysis",
      "topics": [
        "SDA"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "DelayedArray",
    "farver",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "plyr",
    "qvalue",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "trust",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "SDAMS.Rnw",
      "filename": "SDAMS.pdf",
      "title": "SDAMS Vignette",
      "engine": "utils::Sweave",
      "headings": [
        "1 Citation",
        "2 Quick Start",
        "3 Data Input",
        "4 Data Analysis",
        "5 Theory for SDAMS",
        "6 Session Info"
      ],
      "created": "2018-02-01 01:53:48",
      "modified": "2023-07-26 14:11:02",
      "commits": 17
    }
  ],
  "_score": 3.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "sdams",
  "_universes": [
    "bioc",
    "stat-li"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T04:29:25.000Z",
      "distro": "resolute",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/c5169a5645a32ac5b80a37092353c7b30cc714076a30e44c05e2682ab16436e7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-07-04T04:29:44.000Z",
      "distro": "resolute",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/3c8d8c7dfafc8afeecc91acd3a857fe940417931607bb796795afa1dc862dc24",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T04:28:17.000Z",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/fea70cd91d0e10d2a58d32b7bd9527848e37cee08d459fe9c15c551e5bf110cb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-07-04T04:28:10.000Z",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/a337305e43133703da0cb6a09502700fd0a7b8df5b0d5554fd26fa64cf6247c6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-07-04T04:29:42.000Z",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/884c2537d9f10dae02b676a42744839200b3f360660990e58a8ea4e77f1dab88",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T04:27:56.000Z",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/0d1a3d2caf5a53cb9632b9277c8d1c6519403dda8ef3f3ea427d2418bbac4236",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T04:27:53.000Z",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/105d4ad5cf6736d139809ff61f55cd969f1ed806ed156a6731af1805e730d94e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-07-04T04:27:53.000Z",
      "commit": "db34dc944f4eaed61787f0865ca4e313f93c3e1e",
      "fileid": "https://r2.ropensci.org/91b187113bdcaffd723c404fbbaece52bd63ed0ed1df0031e284c6d828098f41",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694779964"
    }
  ]
}