{
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  "Package": "ELMER",
  "Title": "Inferring Regulatory Element Landscapes and Transcription Factor\nNetworks Using Cancer Methylomes",
  "Version": "2.37.0",
  "Authors@R": "c( person(\"Tiago\",\"Chedraoui Silva\", role = c(\"aut\",\"cre\"), email = \"tiagochst@gmail.com\"),\nperson(\"Lijing\", \"Yao\", role = \"aut\", email = \"lijingya@usc.edu\"),\nperson(\"Simon\",\"Coetzee\", role = c(\"aut\"), email = \"Simon.Coetzee@cshs.org\"),\nperson(\"Nicole\", \"Gull\", role = \"ctb\"),\nperson(\"Hui\", \"Shen\", role = \"ctb\"),\nperson(\"Peter\", \"Laird\", role = \"ctb\"),\nperson(\"Peggy\", \"Farnham\", role = \"aut\"),\nperson(\"Dechen\", \"Li\", role = \"ctb\"),\nperson(\"Benjamin\", \"Berman\", role = \"aut\")\n)",
  "Maintainer": "Tiago Chedraoui Silva <tiagochst@gmail.com>",
  "Description": "ELMER is designed to use DNA methylation and gene\nexpression from a large number of samples to infere regulatory\nelement landscape and transcription factor network in primary\ntissue.",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "biocViews": "DNAMethylation, GeneExpression, MotifAnnotation, Software,\nGeneRegulation, Transcription, Network",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:23 UTC",
  "RemoteUrl": "https://github.com/bioc/ELMER",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:45:03 UTC",
    "User": "root"
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  "Author": "Tiago Chedraoui Silva [aut, cre],\nLijing Yao [aut],\nSimon Coetzee [aut],\nNicole Gull [ctb],\nHui Shen [ctb],\nPeter Laird [ctb],\nPeggy Farnham [aut],\nDechen Li [ctb],\nBenjamin Berman [aut]",
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  "_created": "2026-05-30T09:45:03.000Z",
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    "geneexpression",
    "motifannotation",
    "software",
    "generegulation",
    "transcription",
    "network"
  ],
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_exports": [
    "addDistNearestTSS",
    "calculateEnrichement",
    "createBigWigDNAmetArray",
    "createIGVtrack",
    "createMAE",
    "createMotifRelevantTfs",
    "createTSVTemplates",
    "get.diff.meth",
    "get.enriched.motif",
    "get.feature.probe",
    "get.pair",
    "get.permu",
    "get.TFs",
    "getExp",
    "getExpSamples",
    "getGeneID",
    "getMet",
    "getMetSamples",
    "GetNearGenes",
    "getRandomPairs",
    "getRegionNearGenes",
    "getSymbol",
    "getTCGA",
    "getTFBindingSites",
    "getTFtargets",
    "getTSS",
    "heatmapGene",
    "heatmapPairs",
    "metBoxPlot",
    "motif.enrichment.plot",
    "preAssociationProbeFiltering",
    "promoterMeth",
    "render_report",
    "scatter.plot",
    "schematic.plot",
    "TCGA.pipe",
    "TF.rank.plot",
    "TFsurvival.plot"
  ],
  "_help": [
    {
      "page": "addDistNearestTSS",
      "title": "Calculate the distance between probe and gene TSS",
      "topics": [
        "addDistNearestTSS"
      ]
    },
    {
      "page": "addMutCol",
      "title": "Adds mutation information to MAE",
      "topics": [
        "addMutCol"
      ]
    },
    {
      "page": "calcDistNearestTSS",
      "title": "Calculate distance from region to nearest TSS",
      "topics": [
        "calcDistNearestTSS"
      ]
    },
    {
      "page": "calculateEnrichement",
      "title": "Calculate motif Erichment",
      "topics": [
        "calculateEnrichement"
      ]
    },
    {
      "page": "createBigWigDNAmetArray",
      "title": "Create a bigwig file for IGV visualization of DNA methylation data (Array)",
      "topics": [
        "createBigWigDNAmetArray"
      ]
    },
    {
      "page": "createIGVtrack",
      "title": "Create a junction track for IGV visualization of interection",
      "topics": [
        "createIGVtrack"
      ]
    },
    {
      "page": "createMAE",
      "title": "Construct a Multi Assay Experiment for ELMER analysis",
      "topics": [
        "createMAE"
      ]
    },
    {
      "page": "createMotifRelevantTfs",
      "title": "Get family of transcription factors",
      "topics": [
        "createMotifRelevantTfs"
      ]
    },
    {
      "page": "createSummaryDocument",
      "title": "Create summary document for TCGA.pipe function",
      "topics": [
        "createSummaryDocument"
      ]
    },
    {
      "page": "createTSVTemplates",
      "title": "Create examples files for Sample mapping and information used in createMAE function",
      "topics": [
        "createTSVTemplates"
      ]
    },
    {
      "page": "ELMER",
      "title": "ELMER (Enhancer Linking by Methylation/Expression Relationships)",
      "topics": [
        "ELMER"
      ]
    },
    {
      "page": "findMotifRegion",
      "title": "Use Hocomoco motif and homer to identify motifs in a given region",
      "topics": [
        "findMotifRegion"
      ]
    },
    {
      "page": "get.diff.meth",
      "title": "Identify hypo/hyper-methylated CpG sites between two groups (i.e. normal vs tumor samples, treated vs untreated).",
      "topics": [
        "get.diff.meth"
      ]
    },
    {
      "page": "get.enriched.motif",
      "title": "get.enriched.motif to identify the overrepresented motifs in a set of probes (HM450K) regions.",
      "topics": [
        "get.enriched.motif"
      ]
    },
    {
      "page": "get.feature.probe",
      "title": "get.feature.probe to select probes within promoter regions or distal regions.",
      "topics": [
        "get.feature.probe"
      ]
    },
    {
      "page": "get.pair",
      "title": "get.pair to predict enhancer-gene linkages.",
      "topics": [
        "get.pair"
      ]
    },
    {
      "page": "get.permu",
      "title": "get.permu to generate permutation results for calculation of empirical P values for each enhancer-gene linkage.",
      "topics": [
        "get.permu"
      ]
    },
    {
      "page": "Get.Pvalue.p",
      "title": "Calculate empirical Pvalue",
      "topics": [
        "Get.Pvalue.p"
      ]
    },
    {
      "page": "get.tab",
      "title": "summarize MR TF as a binary table with 1 if TF was found in the analysis, 0 if not",
      "topics": [
        "get.tab"
      ]
    },
    {
      "page": "get.tabs",
      "title": "Creating matrix for MR TF heatmap",
      "topics": [
        "get.tabs"
      ]
    },
    {
      "page": "get.TFs",
      "title": "get.TFs to identify regulatory TFs.",
      "topics": [
        "get.TFs"
      ]
    },
    {
      "page": "get450K",
      "title": "get450K to download HM40K DNA methylation data for certain cancer types from TCGA website.  @description get450K is a function to download latest version of HM450K DNA methylation for all samples of certain cancer types from GDC website.",
      "topics": [
        "get450K"
      ]
    },
    {
      "page": "getClinic",
      "title": "getClinic to download clinic data for certain cancer types from TCGA website.",
      "topics": [
        "getClinic"
      ]
    },
    {
      "page": "getExp",
      "title": "Get Gene expression object from MAE",
      "topics": [
        "getExp"
      ]
    },
    {
      "page": "getExpSamples",
      "title": "Get Gene expression object samples from MAE",
      "topics": [
        "getExpSamples"
      ]
    },
    {
      "page": "getGeneID",
      "title": "getGeneID to report gene id from symbol",
      "topics": [
        "getGeneID"
      ]
    },
    {
      "page": "getMet",
      "title": "Get DNA methylation object from MAE",
      "topics": [
        "getMet"
      ]
    },
    {
      "page": "getMetSamples",
      "title": "Get DNA methylation object samples from MAE",
      "topics": [
        "getMetSamples"
      ]
    },
    {
      "page": "GetNearGenes",
      "title": "GetNearGenes to collect nearby genes for one locus.",
      "topics": [
        "GetNearGenes"
      ]
    },
    {
      "page": "getRandomPairs",
      "title": "Get random pairs",
      "topics": [
        "getRandomPairs"
      ]
    },
    {
      "page": "getRegionNearGenes",
      "title": "Identifies nearest genes to a region",
      "topics": [
        "getRegionNearGenes"
      ]
    },
    {
      "page": "getRNAseq",
      "title": "getRNAseq to download all RNAseq data for a certain cancer type from TCGA.",
      "topics": [
        "getRNAseq"
      ]
    },
    {
      "page": "getSymbol",
      "title": "getSymbol to report gene symbol from id",
      "topics": [
        "getSymbol"
      ]
    },
    {
      "page": "getTCGA",
      "title": "getTCGA to download DNA methylation, RNA expression and clinic data for all samples of certain cancer type from TCGA.",
      "topics": [
        "getTCGA"
      ]
    },
    {
      "page": "getTF",
      "title": "Get human TF list from the UNiprot database",
      "topics": [
        "getTF"
      ]
    },
    {
      "page": "getTFBindingSites",
      "title": "Get MR TF binding regions infered by ELMER",
      "topics": [
        "getTFBindingSites"
      ]
    },
    {
      "page": "getTFtargets",
      "title": "Get TF target genes",
      "topics": [
        "getTFtargets"
      ]
    },
    {
      "page": "getTSS",
      "title": "getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.",
      "topics": [
        "getTSS"
      ]
    },
    {
      "page": "heatmapGene",
      "title": "Heatmap for correlation between probes DNA methylation and a single gene expression.",
      "topics": [
        "heatmapGene"
      ]
    },
    {
      "page": "heatmapPairs",
      "title": "Heatmap of pairs gene and probes anti-correlated",
      "topics": [
        "heatmapPairs"
      ]
    },
    {
      "page": "lm_eqn",
      "title": "lable linear regression formula",
      "topics": [
        "lm_eqn"
      ]
    },
    {
      "page": "metBoxPlot",
      "title": "scatter.plot to plot scatter plots between gene expression and DNA methylation.",
      "topics": [
        "metBoxPlot"
      ]
    },
    {
      "page": "motif.enrichment.plot",
      "title": "motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs",
      "topics": [
        "motif.enrichment.plot"
      ]
    },
    {
      "page": "preAssociationProbeFiltering",
      "title": "Filtering probes",
      "topics": [
        "preAssociationProbeFiltering"
      ]
    },
    {
      "page": "promoterMeth",
      "title": "promoterMeth to calculate associations of gene expression with DNA methylation at promoter regions",
      "topics": [
        "promoterMeth"
      ]
    },
    {
      "page": "render_report",
      "title": "Build report for TCGA.pipe function",
      "topics": [
        "render_report"
      ]
    },
    {
      "page": "scatter",
      "title": "scatter",
      "topics": [
        "scatter"
      ]
    },
    {
      "page": "scatter.plot",
      "title": "scatter.plot to plot scatter plots between gene expression and DNA methylation.",
      "topics": [
        "scatter.plot"
      ]
    },
    {
      "page": "schematic.plot",
      "title": "schematic.plot to plot schematic plots showing the locations of genes and probes.",
      "topics": [
        "schematic.plot"
      ]
    },
    {
      "page": "Stat.diff.meth",
      "title": "Stat.diff.meth",
      "topics": [
        "Stat.diff.meth"
      ]
    },
    {
      "page": "Stat.nonpara",
      "title": "U test (non parameter test) for permutation. This is one probe vs nearby gene which is good for computing each probes for nearby genes.",
      "topics": [
        "Stat.nonpara"
      ]
    },
    {
      "page": "Stat.nonpara.permu",
      "title": "Stat.nonpara.permu",
      "topics": [
        "Stat.nonpara.permu"
      ]
    },
    {
      "page": "summarizeTF",
      "title": "Make MR TF binary table",
      "topics": [
        "summarizeTF"
      ]
    },
    {
      "page": "TCGA.pipe",
      "title": "ELMER analysis pipeline for TCGA data.",
      "topics": [
        "TCGA.pipe"
      ]
    },
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