Package: oposSOM 2.30.0

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_2.30.0.tar.gz
oposSOM_2.30.0.zip(r-4.7)oposSOM_2.30.0.zip(r-4.6)oposSOM_2.30.0.zip(r-4.5)
oposSOM_2.30.0.tgz(r-4.6-x86_64)oposSOM_2.30.0.tgz(r-4.6-arm64)oposSOM_2.30.0.tgz(r-4.5-x86_64)oposSOM_2.30.0.tgz(r-4.5-arm64)
oposSOM_2.30.0.tar.gz(r-4.7-arm64)oposSOM_2.30.0.tar.gz(r-4.7-x86_64)oposSOM_2.30.0.tar.gz(r-4.6-arm64)oposSOM_2.30.0.tar.gz(r-4.6-x86_64)
oposSOM_2.30.0.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-release.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

4.34 score 11 scripts 480 downloads 27 mentions 107 exports 73 dependencies

Last updated from:2839a28268 (on RELEASE_3_23). Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR197
linux-devel-arm64WARNING289
linux-devel-x86_64WARNING318
source / vignettesOK267
linux-release-arm64WARNING279
linux-release-x86_64WARNING279
macos-release-arm64WARNING204
macos-release-x86_64WARNING379
macos-oldrel-arm64WARNING457
macos-oldrel-x86_64WARNING487
windows-develWARNING290
windows-releaseWARNING283
windows-oldrelWARNING265
wasm-releaseOK141

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 02 2026.

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