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
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.detectSpotsSamples 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
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
hloefflerwirth/oposSOM documentation built on July 24, 2022, 11:21 p.m.