Package: oposSOM 2.31.0

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_2.31.0.tar.gz
oposSOM_2.31.0.zip(r-4.7)oposSOM_2.31.0.zip(r-4.6)oposSOM_2.31.0.zip(r-4.5)
oposSOM_2.31.0.tgz(r-4.6-x86_64)oposSOM_2.31.0.tgz(r-4.6-arm64)oposSOM_2.31.0.tgz(r-4.5-x86_64)oposSOM_2.31.0.tgz(r-4.5-arm64)
oposSOM_2.31.0.tar.gz(r-4.7-arm64)oposSOM_2.31.0.tar.gz(r-4.7-x86_64)oposSOM_2.31.0.tar.gz(r-4.6-arm64)oposSOM_2.31.0.tar.gz(r-4.6-x86_64)
oposSOM_2.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-2.31.0(bioc 3.24)oposSOM-2.30.0(bioc 3.23)

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

geneexpressiondifferentialexpressiongenesetenrichmentdatarepresentationvisualizationcpp

4.30 score 9 scripts 480 downloads 27 mentions 107 exports 73 dependencies

Last updated from:bd9c5d7b1f. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR174
linux-devel-arm64WARNING293
linux-devel-x86_64WARNING300
source / vignettesOK224
linux-release-arm64WARNING262
linux-release-x86_64WARNING285
macos-release-arm64WARNING161
macos-release-x86_64WARNING330
macos-oldrel-arm64WARNING176
macos-oldrel-x86_64WARNING330
windows-develWARNING251
windows-releaseWARNING251
windows-oldrelWARNING224
wasm-releaseOK130

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:AnnotationDbiapeaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrfastICAfastmapfdrtoolfilelockgenericsgluegraphhmshttrhttr2igraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimenlmeopensslpillarpixmappkgconfigpngprettyunitsprogresspurrrR6rappdirsRcppRcppParallelRCurlrlangRSQLiteS4Vectorsscatterplot3dSeqinfostringistringrsystibbletidyrtidyselecttsneutf8vctrswithrXMLxml2XVector

The oposSOM users guide

Rendered fromVignette.Rnwusingutils::Sweaveon Jun 14 2026.

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