{
  "_id": "6a1b005f1d7bb097a09ff651",
  "Package": "SMITE",
  "Type": "Package",
  "Title": "Significance-based Modules Integrating the Transcriptome and\nEpigenome",
  "Version": "1.41.0",
  "Date": "2021-11-21",
  "Author": "Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally",
  "Maintainer": "Neil Ari Wijetunga <nawijet@gmail.com>, Andrew Damon\nJohnston <Andrew.Johnston@med.einstein.yu.edu>",
  "Description": "This package builds on the Epimods framework which\nfacilitates finding weighted subnetworks (\"modules\") on\nIllumina Infinium 27k arrays using the SpinGlass algorithm, as\nimplemented in the iGraph package. We have created a class of\ngene centric annotations associated with p-values and effect\nsizes and scores from any researchers prior statistical results\nto find functional modules.",
  "License": "GPL (>=2)",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, DifferentialMethylation,\nDifferentialExpression, SystemsBiology,\nNetworkEnrichment,GenomeAnnotation,Network, Sequencing, RNASeq,\nCoverage",
  "URL": "https://github.com/GreallyLab/SMITE",
  "BugReports": "https://github.com/GreallyLab/SMITE/issues",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:37 UTC",
  "RemoteUrl": "https://github.com/bioc/SMITE",
  "RemoteRef": "HEAD",
  "RemoteSha": "1ac1d563a5c6d65675200eecc4f5dddbe457858f",
  "Packaged": {
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    "User": "root"
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  "_published": "2026-05-30T15:21:03.687Z",
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    "differentialmethylation",
    "differentialexpression",
    "systemsbiology",
    "networkenrichment",
    "genomeannotation",
    "network",
    "sequencing",
    "rnaseq",
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    "annotateExpression",
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    "convertGeneIds",
    "extractExpression",
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    "extractModification",
    "extractModSummary",
    "extractModules",
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    "highScores",
    "makePvalueAnnotation",
    "makePvalueObject",
    "normalizePval",
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    "plotDensityPval",
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    "removeModification",
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    "runGOseq",
    "runSpinglass",
    "scorePval",
    "searchGOseq",
    "stoufferTest"
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      "title": "A toy dataset ofcurated RNA-seq to test within SMITE",
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        "pval"
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      "file": "genes_for_conversiontest.rda",
      "class": [
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      ],
      "fields": [
        "genes"
      ],
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      "table": true,
      "tojson": true
    },
    {
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      "title": "A toy dataset of H3k4me1 peaks to test within SMITE",
      "object": "histone_h3k4me1",
      "file": "histone_h3k4me1.rda",
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        "V2",
        "V3"
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      "table": true,
      "tojson": true
    },
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      "name": "hg19_genes",
      "title": "A bed file annotating Refseq genes for the hg19 genome build",
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      "file": "hg19_genes_bed.rda",
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      "table": true,
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    },
    {
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      "object": "methylationdata",
      "file": "methylationdata.rda",
      "class": [
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      ],
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        "V2",
        "V3",
        "V4",
        "V5"
      ],
      "rows": 30000,
      "table": true,
      "tojson": true
    },
    {
      "name": "REACTOME",
      "title": "An Igraph network for REACTOME with nodes as gene symbols",
      "object": "Reactome.Symbol.Igraph",
      "file": "Reactome.Symbol.Igraph.rda",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "test_annotation",
      "title": "A toy PvalueAnnotation",
      "object": "test_annotation_score_data",
      "file": "test_annotation_score_data.rda",
      "class": [
        "PvalueAnnotation"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "SMITE-package",
      "title": "Significance-based Modules Integrating the Transcriptome and Epigenome",
      "topics": [
        "SMITE-package",
        "SMITE"
      ]
    },
    {
      "page": "addShadowText",
      "title": "Add shadow text (a second color bordering the text) to a plot",
      "topics": [
        "addShadowText",
        "addShadowText,ANY-method"
      ]
    },
    {
      "page": "annotateExpression",
      "title": "Adding expression data to a PvalueAnnotation",
      "topics": [
        "annotateExpression",
        "annotateExpression,PvalueAnnotation-method"
      ]
    },
    {
      "page": "annotateModification",
      "title": "Adding modification data to a PvalueAnnotation",
      "topics": [
        "annotateModification",
        "annotateModification,PvalueAnnotation-method"
      ]
    },
    {
      "page": "convertGeneIds",
      "title": "Convert between gene ids",
      "topics": [
        "convertGeneIds",
        "convertGeneIds,character,character,character-method"
      ]
    },
    {
      "page": "curated_expression",
      "title": "A toy dataset ofcurated RNA-seq to test within SMITE",
      "topics": [
        "curated_expressiondata",
        "expression_curated"
      ]
    },
    {
      "page": "extractExpression",
      "title": "View the expression data stored in a PvalueAnnotation",
      "topics": [
        "extractExpression",
        "extractExpression,PvalueAnnotation-method"
      ]
    },
    {
      "page": "extractGOseq",
      "title": "View the GOseq pathway analysis after having run Goseq, or search for a term.",
      "topics": [
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        "extractGOseq,PvalueAnnotation-method",
        "searchGOseq",
        "searchGOseq,PvalueAnnotation-method"
      ]
    },
    {
      "page": "extractModification",
      "title": "Extract some or all loaded modifications or a the summary of combined effects",
      "topics": [
        "extractModification",
        "extractModification,PvalueAnnotation-method",
        "extractModSummary",
        "extractModSummary,PvalueAnnotation-method"
      ]
    },
    {
      "page": "extractModules",
      "title": "View specific modules within a PvalueAnnotation",
      "topics": [
        "extractModules",
        "extractModules,PvalueAnnotation-method"
      ]
    },
    {
      "page": "extractScores",
      "title": "Extract scores for all genes",
      "topics": [
        "extractScores",
        "extractScores,PvalueAnnotation-method"
      ]
    },
    {
      "page": "genes_for_conversiontest",
      "title": "A small set of RefSeq genes for converting",
      "topics": [
        "genes",
        "genes_for_conversiontest"
      ]
    },
    {
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      "title": "A bed file annotating Refseq genes for the hg19 genome build",
      "topics": [
        "hg19_genes",
        "hg19_genes_bed"
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    },
    {
      "page": "highScores",
      "title": "Generate a vector of the highest scoring genes",
      "topics": [
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        "highScores,PvalueAnnotation-method"
      ]
    },
    {
      "page": "histone_h3k4me1",
      "title": "A toy dataset of H3k4me1 peaks to test within SMITE",
      "topics": [
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        "histone_h3k4me1"
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    },
    {
      "page": "makePvalueAnnotation",
      "title": "Initialize a PvalueAnnotation",
      "topics": [
        "makePvalueAnnotation",
        "makePvalueAnnotation,ANY-method"
      ]
    },
    {
      "page": "makePvalueObject",
      "title": "Function to make a PvalueObject within a PvalueAnnotation",
      "topics": [
        "makePvalueObject",
        "makePvalueObject,PvalueAnnotation-method"
      ]
    },
    {
      "page": "methylationdata",
      "title": "A toy dataset of DNA methylation to test within SMITE",
      "topics": [
        "methylation",
        "methylationdata"
      ]
    },
    {
      "page": "normalizePval",
      "title": "This function normalizes p-values (Scores) that are otherwise on different scales.",
      "topics": [
        "normalizePval",
        "normalizePval,PvalueAnnotation-method"
      ]
    },
    {
      "page": "plotCompareScores",
      "title": "Compare two genomic features by score and display them in a hexbin plot",
      "topics": [
        "plotCompareScores",
        "plotCompareScores,PvalueAnnotation-method"
      ]
    },
    {
      "page": "plotDensityPval",
      "title": "Plot the density of the combined scores stored in a PvalueObject",
      "topics": [
        "plotDensityPval",
        "plotDensityPval,PvalueAnnotation-method"
      ]
    },
    {
      "page": "plotModule",
      "title": "Plot a specific module after running Spinglass algorithm",
      "topics": [
        "plotModule",
        "plotModule,PvalueAnnotation-method"
      ]
    },
    {
      "page": "Reactome.Symbol.Igraph",
      "title": "An Igraph network for REACTOME with nodes as gene symbols",
      "topics": [
        "REACTOME",
        "Reactome.Symbol.Igraph"
      ]
    },
    {
      "page": "removeModification",
      "title": "A function to \"unload\" a modification that has already been added.",
      "topics": [
        "removeModification",
        "removeModification,PvalueAnnotation-method"
      ]
    },
    {
      "page": "runBioNet",
      "title": "Perform BioNet Analysis on a PvalueAnnotation",
      "topics": [
        "runBioNet",
        "runBioNet,PvalueAnnotation-method"
      ]
    },
    {
      "page": "runGOseq",
      "title": "Run a GoSeq pathway analysis",
      "topics": [
        "runGOseq",
        "runGOseq,PvalueAnnotation-method"
      ]
    },
    {
      "page": "runSpinglass",
      "title": "Run Spinglass algorithm on a Scored PvalueAnnotation",
      "topics": [
        "runSpinglass",
        "runSpinglass,PvalueAnnotation-method"
      ]
    },
    {
      "page": "scorePval",
      "title": "Making a single combined score for each gene",
      "topics": [
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        "scorePval,PvalueAnnotation-method"
      ]
    },
    {
      "page": "stoufferTest",
      "title": "Stouffer's Test",
      "topics": [
        "stoufferTest",
        "stoufferTest,vector-method"
      ]
    },
    {
      "page": "test_annotation_score_data",
      "title": "A toy PvalueAnnotation",
      "topics": [
        "test_annotation",
        "test_annotation_score_data"
      ]
    }
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    "rmarkdown",
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    "xml2",
    "XVector",
    "yaml"
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  "_vignettes": [
    {
      "source": "SMITE.Rmd",
      "filename": "SMITE.html",
      "title": "SMITE Vignette",
      "author": "Andrew D. Johnston, N. Ari Wijetunga, and John M. Greally",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2016-02-12 23:53:53",
      "modified": "2020-01-30 11:34:22",
      "commits": 3
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