Package: oposSOM 2.23.0

Henry Loeffler-Wirth

oposSOM: Comprehensive analysis of transcriptome data

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

Authors:Henry Loeffler-Wirth <[email protected]>, Hoang Thanh Le <[email protected]> and Martin Kalcher <[email protected]>

oposSOM_2.23.0.tar.gz
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oposSOM.pdf |oposSOM.html✨
oposSOM/json (API)
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Peer review:

On BioConductor:oposSOM-2.23.0(bioc 3.20)oposSOM-2.22.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

99 exports 0.91 score 78 dependencies 27 mentions 52 downloads

Last updated 2 months agofrom:2fb87043b5

Exports:_oposSOM_calculateDelta_oposSOM_calculateEuclideanDistances_oposSOM_calculateNeighborhoodMatrix_oposSOM_matrixToCodebookMatrixbiomart.availablecalculateDeltacalculateEuclideanDistancescalculateNeighborhoodMatrixcirclecol.pixcolor.palette.discretecolor.palette.heatmapscolor.palette.portraitsGeneSet.FisherGeneSet.maxmeanget.beta.statisticget.neighborsGet.Running.Averageheatmapheatmap.A4matrixToCodebookMatrixmodules.chromosomesmodules.CSV.sheetsmodules.profilesmodules.relationsmodules.report.sheetsnewProgressBaropossom.newopossom.runpathway.expression.mappingpipeline.affymetrixQualityCheckpipeline.cancerHallmarkspipeline.checkInputParameterspipeline.chromosomeExpressionReportspipeline.detectEnsemblDatasetpipeline.detectSpotsModulespipeline.detectSpotsSamplespipeline.differenceAnalysespipeline.diffExpressionStatisticspipeline.entropyProfilespipeline.geneListspipeline.generateSOMpipeline.genesetOverviewspipeline.genesetProfilesAndMapspipeline.genesetStatisticModulespipeline.genesetStatisticSamplespipeline.groupAnalysispipeline.groupAssignmentpipeline.groupSpecificGenesetspipeline.htmlDifferencesSummarypipeline.htmlGenesetAnalysispipeline.htmlGroupSummarypipeline.htmlModuleSummarypipeline.htmlPsfAnalysispipeline.htmlSampleSummarypipeline.htmlSummarypipeline.moduleCorrelationMappipeline.patAssignmentpipeline.prepareAnnotationpipeline.prepareIndatapipeline.PSFcalculationpipeline.PSFoutputpipeline.qualityCheckpipeline.sampleExpressionPortraitspipeline.sampleSimilarityAnalysisCorpipeline.sampleSimilarityAnalysisEDpipeline.sampleSimilarityAnalysisICApipeline.sampleSimilarityAnalysisSOMpipeline.summarySheetsGroupspipeline.summarySheetsModulespipeline.summarySheetsPATspipeline.summarySheetsSamplespipeline.supportingMapspipeline.topologyProfilesplot.psf.pathway.keggrestplot.psf.titlepagepsf.flowpsf.overview.heatmapspsf.report.sheetsQuantile.NormalizationradarchartSample.GSZSmooth.Matrixsom.linear.initsom.linear.init.subdatasom.trainingsom.training.phasesort.labelutil.callutil.catutil.fatalutil.infoutil.loadutil.logutil.progressutil.progress.terminateutil.saveutil.warnworkspace.check

Dependencies:AnnotationDbiapeaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrfansifastICAfastmapfdrtoolfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluegraphhmshttrhttr2igraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimenlmeopensslpillarpixmappkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRcppRcppParallelRCurlrlangRSQLiteS4Vectorsscatterplot3dstringistringrsystibbletidyrtidyselecttsneUCSC.utilsutf8vctrswithrXMLxml2XVectorzlibbioc