API for hloefflerwirth/oposSOM
Comprehensive analysis of transcriptome data
| Global functions | |
|---|---|
| GeneSet.Fisher | Source code |
| GeneSet.maxmean | Source code |
| Get.Running.Average | Source code |
| Quantile.Normalization | Source code |
| Sample.GSZ | Source code |
| biomart.available | Source code |
| by.minicluster | Source code |
| calculateDelta | Source code |
| calculateEuclideanDistances | Source code |
| calculateNeighborhoodMatrix | Source code |
| chunk.apply.rows | Source code |
| chunk.sapply | Source code |
| circle | Source code |
| col.pix | Source code |
| color.palette.discrete | Source code |
| color.palette.interlace | Source code |
| eval_formulas | Source code |
| get.beta.statistic | Source code |
| get.neighbors | Source code |
| matrixToCodebookMatrix | Source code |
| modules.CSV.sheets | Source code |
| modules.chromosomes | Source code |
| modules.profiles | Source code |
| modules.relations | Source code |
| modules.report.sheets | Source code |
| oposSOM | Man page |
| oposSOM-package | Man page |
| opossom.genesets | Man page |
| opossom.new | Man page Source code |
| opossom.run | Man page Source code |
| opossom.tissues | Man page |
| pipeline.PSFcalculation | Source code |
| pipeline.PSFoutput | Source code |
| pipeline.affymetrixQualityCheck | Source code |
| pipeline.cancerHallmarks | Source code |
| pipeline.checkInputParameters | Source code |
| pipeline.chromosomeExpressionReports | Source code |
| pipeline.detectCorrelationModules | Source code |
| pipeline.detectDMapModules | Source code |
| pipeline.detectEnsemblDataset | Source code |
| pipeline.detectGroupOverexpressionModules | Source code |
| pipeline.detectKMeansModules | Source code |
| pipeline.detectOverexpressionModules | Source code |
| pipeline.detectSpotsModules | Source code |
| pipeline.detectUnderexpressionModules | Source code |
| pipeline.diffExpressionStatistics | Source code |
| pipeline.differenceAnalyses | Source code |
| pipeline.entropyProfiles | Source code |
| pipeline.geneLists | Source code |
| pipeline.generateSOM | Source code |
| pipeline.genesetOverviews | Source code |
| pipeline.genesetProfilesAndMaps | Source code |
| pipeline.genesetStatisticModules | Source code |
| pipeline.genesetStatisticSamples | Source code |
| pipeline.groupAnalysis | Source code |
| pipeline.groupAssignment | Source code |
| pipeline.groupSpecificGenesets | Source code |
| pipeline.htmlDifferencesSummary | Source code |
| pipeline.htmlGenesetAnalysis | Source code |
| pipeline.htmlGroupSummary | Source code |
| pipeline.htmlModuleSummary | Source code |
| pipeline.htmlPsfAnalysis | Source code |
| pipeline.htmlSampleSummary | Source code |
| pipeline.htmlSummary | Source code |
| pipeline.moduleCorrelationMap | Source code |
| pipeline.patAssignment | Source code |
| pipeline.prepareAnnotation | Source code |
| pipeline.prepareIndata | Source code |
| pipeline.qualityCheck | Source code |
| pipeline.sampleExpressionPortraits | Source code |
| pipeline.sampleSimilarityAnalysisCor | Source code |
| pipeline.sampleSimilarityAnalysisED | Source code |
| pipeline.sampleSimilarityAnalysisICA | Source code |
| pipeline.sampleSimilarityAnalysisSOM | Source code |
| pipeline.summarySheetsGroups | Source code |
| pipeline.summarySheetsModules | Source code |
| pipeline.summarySheetsPATs | Source code |
| pipeline.summarySheetsSamples | Source code |
| pipeline.supportingMaps | Source code |
| pipeline.topologyProfiles | Source code |
| plot.psf.pathway.keggrest | Source code |
| plot.psf.titlepage | Source code |
| psf.overview.heatmaps | Source code |
| psf.report.sheets | Source code |
| psf_processing | Source code |
| som.linear.init | Source code |
| som.training | Source code |
| som.training.phase | Source code |
| sort.label | Source code |
| spot.borders | Source code |
| util.call | Source code |
| util.cat | Source code |
| util.fatal | Source code |
| util.info | Source code |
| util.log | Source code |
| util.progress | Source code |
| util.progress.terminate | Source code |
| util.warn | Source code |
| workspace.check | Source code |
