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'))

Peer review:

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 269 downloads 27 mentions 107 exports 77 dependencies

Last updated 3 months agofrom:a26ada95d2. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKDec 29 2024
R-4.5-win-x86_64WARNINGDec 31 2024
R-4.5-linux-x86_64WARNINGDec 29 2024
R-4.4-win-x86_64WARNINGDec 31 2024
R-4.4-mac-x86_64WARNINGDec 29 2024
R-4.4-mac-aarch64WARNINGDec 29 2024
R-4.3-win-x86_64WARNINGDec 31 2024
R-4.3-mac-x86_64WARNINGDec 29 2024
R-4.3-mac-aarch64WARNINGDec 29 2024

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 Dec 29 2024.

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