{
  "_id": "6a1ad2971d7bb097a09e2ffd",
  "Package": "EMDomics",
  "Title": "Earth Mover's Distance for Differential Analysis of Genomics\nData",
  "Description": "The EMDomics algorithm is used to perform a supervised\nmulti-class analysis to measure the magnitude and statistical\nsignificance of observed continuous genomics data between\ngroups. Usually the data will be gene expression values from\narray-based or sequence-based experiments, but data from other\ntypes of experiments can also be analyzed (e.g. copy number\nvariation). Traditional methods like Significance Analysis of\nMicroarrays (SAM) and Linear Models for Microarray Data (LIMMA)\nuse significance tests based on summary statistics (mean and\nstandard deviation) of the distributions. This approach lacks\npower to identify expression differences between groups that\nshow high levels of intra-group heterogeneity. The Earth\nMover's Distance (EMD) algorithm instead computes the \"work\"\nneeded to transform one distribution into another, thus\nproviding a metric of the overall difference in shape between\ntwo distributions. Permutation of sample labels is used to\ngenerate q-values for the observed EMD scores. This package\nalso incorporates the Komolgorov-Smirnov (K-S) test and the\nCramer von Mises test (CVM), which are both common distribution\ncomparison tests.",
  "Version": "2.43.0",
  "biocViews": "Software, DifferentialExpression, GeneExpression, Microarray",
  "Authors@R": "c( person(\"Sadhika\", \"Malladi\", email=\"contact@sadhikamalladi.com\", role=c(\"aut\",\"cre\")),\nperson(\"Daniel\", \"Schmolze\", email=\"emd@schmolze.com\",\nrole=c(\"aut\",\"cre\")), person(\"Andrew\", \"Beck\",\nemail=\"abeck2@bidmc.harvard.edu\", role=\"aut\"), person(\"Sheida\",\n\"Nabavi\", email=\"sheida_nabavi@hms.harvard.edu\", role=\"aut\"))",
  "Maintainer": "Sadhika Malladi <contact@sadhikamalladi.com> and Daniel\nSchmolze <emd@schmolze.com>",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Author": "Sadhika Malladi [aut, cre], Daniel Schmolze [aut, cre], Andrew\nBeck [aut], Sheida Nabavi [aut]",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:18 UTC",
  "RemoteUrl": "https://github.com/bioc/EMDomics",
  "RemoteRef": "HEAD",
  "RemoteSha": "5b37735396610274330cc046d212adea81249c0b",
  "Packaged": {
    "Date": "2026-05-30 08:34:13 UTC",
    "User": "root"
  },
  "MD5sum": "2ee1f4a1b9a1b725cf51cdfbdde7ac1b",
  "_user": "bioc",
  "_type": "src",
  "_file": "EMDomics_2.43.0.tar.gz",
  "_fileid": "31f529037afff5af17ecd467c28a83231a29352f340eef22f23a67ab4416744e",
  "_filesize": 736600,
  "_sha256": "31f529037afff5af17ecd467c28a83231a29352f340eef22f23a67ab4416744e",
  "_created": "2026-05-30T08:34:13.000Z",
  "_published": "2026-05-30T12:05:43.116Z",
  "_jobs": [
    {
      "job": 78636888821,
      "time": 138,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306875208"
    },
    {
      "job": 78636888804,
      "time": 228,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306883846"
    },
    {
      "job": 78636888801,
      "time": 209,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306882158"
    },
    {
      "job": 78636888806,
      "time": 153,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308041916"
    },
    {
      "job": 78636888811,
      "time": 129,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308039440"
    },
    {
      "job": 78636755100,
      "time": 161,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306861937"
    },
    {
      "job": 78636888815,
      "time": 110,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306872595"
    },
    {
      "job": 78636888813,
      "time": 136,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306874938"
    },
    {
      "job": 78636888817,
      "time": 116,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306873199"
    },
    {
      "job": 78636888819,
      "time": 133,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306874695"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/EMDomics",
  "_commit": {
    "id": "5b37735396610274330cc046d212adea81249c0b",
    "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": 1777380078
  },
  "_maintainer": {
    "name": "Sadhika Malladi",
    "email": "emd@schmolze.com"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.2.1",
      "role": "Depends"
    },
    {
      "package": "emdist",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "CDFt",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.43.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.42.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "differentialexpression",
    "geneexpression",
    "microarray"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 432,
    "source": "https://www.bioconductor.org/packages/stats/bioc/EMDomics"
  },
  "_mentions": 5,
  "_searchresults": 25,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/EMDomics.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.99.0",
      "date": "2014-11-15"
    },
    {
      "version": "0.99.1",
      "date": "2015-02-19"
    }
  ],
  "_exports": [
    "calculate_cvm",
    "calculate_cvm_gene",
    "calculate_emd",
    "calculate_emd_gene",
    "calculate_ks",
    "calculate_ks_gene",
    "CVMomics",
    "EMDomics",
    "KSomics",
    "plot_cvm_density",
    "plot_cvmnull",
    "plot_cvmperms",
    "plot_emd_density",
    "plot_emdnull",
    "plot_emdperms",
    "plot_ks_density",
    "plot_ksnull",
    "plot_ksperms"
  ],
  "_help": [
    {
      "page": "emdomics-package",
      "title": "Earth Mover's Distance algorithm for differential analysis of genomics data.",
      "topics": [
        "emdomics-package"
      ]
    },
    {
      "page": "calculate_cvm",
      "title": "Cramer von Mises for differential analysis of genomics data",
      "topics": [
        "calculate_cvm"
      ]
    },
    {
      "page": "calculate_cvm_gene",
      "title": "Calculate CVM score for a single gene",
      "topics": [
        "calculate_cvm_gene"
      ]
    },
    {
      "page": "calculate_emd",
      "title": "Earth Mover's Distance for differential analysis of genomics data",
      "topics": [
        "calculate_emd"
      ]
    },
    {
      "page": "calculate_emd_gene",
      "title": "Calculate EMD score for a single gene",
      "topics": [
        "calculate_emd_gene"
      ]
    },
    {
      "page": "calculate_ks",
      "title": "Calculate the Komolgorov-Smirnov test statistic and q-values for differential gene expression analysis.",
      "topics": [
        "calculate_ks"
      ]
    },
    {
      "page": "calculate_ks_gene",
      "title": "Calculate KS score for a single gene",
      "topics": [
        "calculate_ks_gene"
      ]
    },
    {
      "page": "CVMomics",
      "title": "Create an CVMomics object",
      "topics": [
        "CVMomics"
      ]
    },
    {
      "page": "EMDomics",
      "title": "Create an EMDomics object",
      "topics": [
        "EMDomics"
      ]
    },
    {
      "page": "KSomics",
      "title": "Create an KSomics object",
      "topics": [
        "KSomics"
      ]
    },
    {
      "page": "plot_cvm_density",
      "title": "Plot distributions and CVM score for a gene.",
      "topics": [
        "plot_cvm_density"
      ]
    },
    {
      "page": "plot_cvmnull",
      "title": "Plot null distribution of permuted cvm scores vs. calculated cvm scores.",
      "topics": [
        "plot_cvmnull"
      ]
    },
    {
      "page": "plot_cvmperms",
      "title": "Plot histogram of CVM scores calculated via random permutation.",
      "topics": [
        "plot_cvmperms"
      ]
    },
    {
      "page": "plot_emd_density",
      "title": "Plot distributions and EMD score for a gene.",
      "topics": [
        "plot_emd_density"
      ]
    },
    {
      "page": "plot_emdnull",
      "title": "Plot null distribution of permuted EMD scores vs. calculated EMD scores.",
      "topics": [
        "plot_emdnull"
      ]
    },
    {
      "page": "plot_emdperms",
      "title": "Plot histogram of EMD scores calculated via random permutation.",
      "topics": [
        "plot_emdperms"
      ]
    },
    {
      "page": "plot_ks_density",
      "title": "Plot distributions and KS score for a gene.",
      "topics": [
        "plot_ks_density"
      ]
    },
    {
      "page": "plot_ksnull",
      "title": "Plot null distribution of permuted ks scores vs. calculated ks scores.",
      "topics": [
        "plot_ksnull"
      ]
    },
    {
      "page": "plot_ksperms",
      "title": "Plot histogram of KS scores calculated via random permutation.",
      "topics": [
        "plot_ksperms"
      ]
    }
  ],
  "_rundeps": [
    "BH",
    "BiocParallel",
    "CDFt",
    "cli",
    "codetools",
    "cpp11",
    "emdist",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lambda.r",
    "lifecycle",
    "matrixStats",
    "preprocessCore",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "snow",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "EMDomics.Rmd",
      "filename": "EMDomics.html",
      "title": "EMDomics Vignette",
      "author": "Sadhika Malladi and Daniel Schmolze",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Welcome",
        "Earth Mover's Distance",
        "Analyzing Significance",
        "Visualization",
        "Wrapping Up",
        "Session Info"
      ],
      "created": "2015-04-14 17:06:48",
      "modified": "2015-07-24 18:54:15",
      "commits": 3
    }
  ],
  "_score": 4.3979400086720375,
  "_indexed": true,
  "_nocasepkg": "emdomics",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.43.0",
      "date": "2026-05-30T08:37:30.000Z",
      "distro": "noble",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "acc7e8431e6c072a68b2717f5fef124c7d25d8c85de08dea30c308b5aaaca836",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.43.0",
      "date": "2026-05-30T08:37:14.000Z",
      "distro": "noble",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "f9f406322dc34b0bd9e9a80673d11ecb05af771d4dfd48605c4b733bacb2085e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.43.0",
      "date": "2026-05-30T12:04:34.000Z",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "31ab411bfe68633a50d913878f24e6dc718ac12d967ea92ea97805815f647800",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.43.0",
      "date": "2026-05-30T12:04:14.000Z",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "23e3d222dcaa2f91db1721e3686f0689a795f5551a31587c6d74310ad653db28",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.43.0",
      "date": "2026-05-30T08:36:20.000Z",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "02eaf9801a8db1f055a31ba3fc9d56ef9b69ce8ac84fdf965e64697d0e649048",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.43.0",
      "date": "2026-05-30T08:35:49.000Z",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "f42fcd4597dad72671df4e621eaef903407c1fce4855ab34e113ebbc08c05e79",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.43.0",
      "date": "2026-05-30T08:35:33.000Z",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "99111b0bb641692014b6413c97bd17f4d2536c6dc57221e809628a795926d32f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.43.0",
      "date": "2026-05-30T08:35:46.000Z",
      "commit": "5b37735396610274330cc046d212adea81249c0b",
      "fileid": "e1f0268af38e4966c9a416a859bf20e0892e676d4702d2eb03b5dea3fad61008",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679302289"
    }
  ]
}