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
calculateDelta	Source code
calculateEuclideanDistances	Source code
calculateNeighborhoodMatrix	Source code
circle	Source code
col.pix	Source code
color.palette.discrete	Source code
color.palette.interlace	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
pathway.expression.mapping	Source code
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
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.load	Source code
util.log	Source code
util.progress	Source code
util.progress.terminate	Source code
util.save	Source code
util.warn	Source code
workspace.check	Source code