Package: oposSOM 2.25.0

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]>

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oposSOM.pdf |oposSOM.html✨
oposSOM/json (API)
NEWS

# Install 'oposSOM' in R:
install.packages('oposSOM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:oposSOM-2.25.0(bioc 3.21)oposSOM-2.24.0(bioc 3.20)

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

geneexpressiondifferentialexpressiongenesetenrichmentdatarepresentationvisualizationcpp

4.48 score 7 scripts 290 downloads 27 mentions 107 exports 77 dependencies

Last updated 4 months agofrom:a26ada95d2. Checks:1 OK, 10 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-win-x86_64WARNINGJan 28 2025
R-4.5-mac-x86_64WARNINGJan 28 2025
R-4.5-mac-aarch64WARNINGJan 28 2025
R-4.5-linux-x86_64WARNINGJan 28 2025
R-4.4-win-x86_64WARNINGJan 28 2025
R-4.4-mac-x86_64WARNINGJan 28 2025
R-4.4-mac-aarch64WARNINGJan 28 2025
R-4.3-win-x86_64WARNINGJan 28 2025
R-4.3-mac-x86_64WARNINGJan 28 2025
R-4.3-mac-aarch64WARNINGJan 28 2025

Exports:_oposSOM_calculateDelta_oposSOM_calculateEuclideanDistances_oposSOM_calculateNeighborhoodMatrix_oposSOM_matrixToCodebookMatrixbiomart.availablecalculateDeltacalculateEuclideanDistancescalculateNeighborhoodMatrixcirclecol.pixcolor.palette.discretecolor.palette.heatmapscolor.palette.interlacecolor.palette.portraitscolor.palette.portraits.cbsGeneSet.FisherGeneSet.maxmeanget.beta.statisticget.neighborsGet.Running.Averageheatmapheatmap.A4matrixToCodebookMatrixmodules.chromosomesmodules.CSV.sheetsmodules.profilesmodules.relationsmodules.report.sheetsnewProgressBaropossom.newopossom.runpathway.expression.mappingpipeline.affymetrixQualityCheckpipeline.cancerHallmarkspipeline.checkInputParameterspipeline.chromosomeExpressionReportspipeline.detectCorrelationModulespipeline.detectDMapModulespipeline.detectEnsemblDatasetpipeline.detectGroupOverexpressionModulespipeline.detectKMeansModulespipeline.detectOverexpressionModulespipeline.detectSpotsModulespipeline.detectUnderexpressionModulespipeline.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.labelspot.bordersutil.callutil.catutil.fatalutil.infoutil.loadutil.logutil.progressutil.progress.terminateutil.saveutil.warnworkspace.check

Dependencies:AnnotationDbiapeaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrfansifastICAfastmapfdrtoolfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluegraphhmshttrhttr2igraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimenlmeopensslpillarpixmappkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRcppRcppParallelRCurlrlangRSQLiteS4Vectorsscatterplot3dstringistringrsystibbletidyrtidyselecttsneUCSC.utilsutf8vctrswithrXMLxml2XVector

The oposSOM users guide

Rendered fromVignette.Rnwusingutils::Sweaveon Jan 28 2025.

Last update: 2021-01-14
Started: 2014-07-01