Example data: transctiptome of healthy human tissue samples | Setting up the environment | Browsing the results | Parameter settings | Recommended SOM size and runtime estimation | Biomart database settings | Citing oposSOM | Details
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
oposSOM/json (API)
| # Install 'oposSOM' in R: |
| install.packages('oposSOM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- opossom.genesets - Additional literature genesets
- opossom.tissues - Example data set.
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
Last updated from:bd9c5d7b1f. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 210 | ||
| linux-devel-arm64 | WARNING | 331 | ||
| linux-devel-x86_64 | WARNING | 329 | ||
| source / vignettes | OK | 262 | ||
| linux-release-arm64 | WARNING | 292 | ||
| linux-release-x86_64 | WARNING | 361 | ||
| macos-release-arm64 | WARNING | 423 | ||
| macos-release-x86_64 | WARNING | 572 | ||
| macos-oldrel-arm64 | WARNING | 160 | ||
| macos-oldrel-x86_64 | WARNING | 453 | ||
| windows-devel | WARNING | 289 | ||
| windows-release | WARNING | 247 | ||
| windows-oldrel | WARNING | 235 | ||
| wasm-release | OK | 158 |
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Comprehensive analysis of transciptome data | oposSOM-package oposSOM |
| Additional literature genesets | opossom.genesets |
| Initialize the oposSOM pipeline. | opossom.new |
| Execute the oposSOM pipeline. | opossom.run |
| Example data set. | opossom.tissues |
