{
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  "Package": "oposSOM",
  "Title": "Comprehensive analysis of transcriptome data",
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  "Description": "This package translates microarray expression data into\nmetadata of reduced dimension. It provides various\nsample-centered and group-centered visualizations, sample\nsimilarity analyses and functional enrichment analyses. The\nunderlying SOM algorithm combines feature clustering,\nmultidimensional scaling and dimension reduction, along with\nstrong visualization capabilities. It enables extraction and\ndescription of functional expression modules inherent in the\ndata.",
  "License": "GPL (>=2)",
  "Author": "Henry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>, Hoang Thanh\nLe <le@izbi.uni-leipzig.de> and Martin Kalcher\n<mkalcher@porkbox.net>",
  "Maintainer": "Henry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>",
  "URL": "http://som.izbi.uni-leipzig.de",
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    "genesetenrichment",
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    "name": "Bioconductor",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "_oposSOM_calculateEuclideanDistances",
    "_oposSOM_calculateNeighborhoodMatrix",
    "_oposSOM_matrixToCodebookMatrix",
    "biomart.available",
    "calculateDelta",
    "calculateEuclideanDistances",
    "calculateNeighborhoodMatrix",
    "circle",
    "col.pix",
    "color.palette.discrete",
    "color.palette.heatmaps",
    "color.palette.interlace",
    "color.palette.portraits",
    "color.palette.portraits.cbs",
    "GeneSet.Fisher",
    "GeneSet.maxmean",
    "get.beta.statistic",
    "get.neighbors",
    "Get.Running.Average",
    "heatmap",
    "heatmap.A4",
    "matrixToCodebookMatrix",
    "modules.chromosomes",
    "modules.CSV.sheets",
    "modules.profiles",
    "modules.relations",
    "modules.report.sheets",
    "newProgressBar",
    "opossom.new",
    "opossom.run",
    "pathway.expression.mapping",
    "pipeline.affymetrixQualityCheck",
    "pipeline.cancerHallmarks",
    "pipeline.checkInputParameters",
    "pipeline.chromosomeExpressionReports",
    "pipeline.detectCorrelationModules",
    "pipeline.detectDMapModules",
    "pipeline.detectEnsemblDataset",
    "pipeline.detectGroupOverexpressionModules",
    "pipeline.detectKMeansModules",
    "pipeline.detectOverexpressionModules",
    "pipeline.detectSpotsModules",
    "pipeline.detectUnderexpressionModules",
    "pipeline.differenceAnalyses",
    "pipeline.diffExpressionStatistics",
    "pipeline.entropyProfiles",
    "pipeline.geneLists",
    "pipeline.generateSOM",
    "pipeline.genesetOverviews",
    "pipeline.genesetProfilesAndMaps",
    "pipeline.genesetStatisticModules",
    "pipeline.genesetStatisticSamples",
    "pipeline.groupAnalysis",
    "pipeline.groupAssignment",
    "pipeline.groupSpecificGenesets",
    "pipeline.htmlDifferencesSummary",
    "pipeline.htmlGenesetAnalysis",
    "pipeline.htmlGroupSummary",
    "pipeline.htmlModuleSummary",
    "pipeline.htmlPsfAnalysis",
    "pipeline.htmlSampleSummary",
    "pipeline.htmlSummary",
    "pipeline.moduleCorrelationMap",
    "pipeline.patAssignment",
    "pipeline.prepareAnnotation",
    "pipeline.prepareIndata",
    "pipeline.PSFcalculation",
    "pipeline.PSFoutput",
    "pipeline.qualityCheck",
    "pipeline.sampleExpressionPortraits",
    "pipeline.sampleSimilarityAnalysisCor",
    "pipeline.sampleSimilarityAnalysisED",
    "pipeline.sampleSimilarityAnalysisICA",
    "pipeline.sampleSimilarityAnalysisSOM",
    "pipeline.summarySheetsGroups",
    "pipeline.summarySheetsModules",
    "pipeline.summarySheetsPATs",
    "pipeline.summarySheetsSamples",
    "pipeline.supportingMaps",
    "pipeline.topologyProfiles",
    "plot.psf.pathway.keggrest",
    "plot.psf.titlepage",
    "psf.flow",
    "psf.overview.heatmaps",
    "psf.report.sheets",
    "Quantile.Normalization",
    "radarchart",
    "Sample.GSZ",
    "Smooth.Matrix",
    "som.linear.init",
    "som.linear.init.subdata",
    "som.training",
    "som.training.phase",
    "sort.label",
    "spot.borders",
    "util.call",
    "util.cat",
    "util.fatal",
    "util.info",
    "util.load",
    "util.log",
    "util.progress",
    "util.progress.terminate",
    "util.save",
    "util.warn",
    "workspace.check"
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  "_datasets": [
    {
      "name": "opossom.genesets",
      "title": "Additional literature genesets",
      "object": "opossom.genesets",
      "file": "opossom.genesets.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
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      "name": "opossom.tissues",
      "title": "Example data set.",
      "object": "opossom.tissues",
      "file": "opossom.tissues.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "liver",
        "kidney cortex",
        "thyroid gland",
        "small intestine",
        "prostate",
        "tongue",
        "testis",
        "skeletal muscle",
        "bone marrow",
        "lymph node",
        "accumbens",
        "cerebral cortex"
      ],
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      "title": "Comprehensive analysis of transciptome data",
      "topics": [
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        "oposSOM"
      ]
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    {
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      "title": "Additional literature genesets",
      "topics": [
        "opossom.genesets"
      ]
    },
    {
      "page": "opossom.new",
      "title": "Initialize the oposSOM pipeline.",
      "topics": [
        "opossom.new"
      ]
    },
    {
      "page": "opossom.run",
      "title": "Execute the oposSOM pipeline.",
      "topics": [
        "opossom.run"
      ]
    },
    {
      "page": "opossom.tissues",
      "title": "Example data set.",
      "topics": [
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      ]
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      "source": "Vignette.Rnw",
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      "title": "The oposSOM users guide",
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      "headings": [
        "Example data: transctiptome of healthy human tissue samples",
        "Setting up the environment",
        "Browsing the results",
        "Parameter settings",
        "Recommended SOM size and runtime estimation",
        "Biomart database settings",
        "Citing oposSOM",
        "Details"
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      "created": "2014-07-01 20:38:11",
      "modified": "2021-01-14 15:56:22",
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