Package: RFLOMICS 1.5.0

Nadia Bessoltane

RFLOMICS: Interactive web application for Omics-data analysis

R-package with shiny interface, provides a framework for the analysis of transcriptomics, proteomics and/or metabolomics data. The interface offers a guided experience for the user, from the definition of the experimental design to the integration of several omics table together. A report can be generated with all settings and analysis results.

Authors:Nadia Bessoltane [aut, cre], Delphine Charif [aut], Audrey Hulot [aut], Christine Paysant-Leroux [aut], Gwendal Cueff [aut]

RFLOMICS_1.5.0.tar.gz
RFLOMICS_1.5.0.zip(r-4.7)RFLOMICS_1.5.0.zip(r-4.6)RFLOMICS_1.5.0.zip(r-4.5)
RFLOMICS_1.5.0.tgz(r-4.6-any)RFLOMICS_1.5.0.tgz(r-4.5-any)
RFLOMICS_1.5.0.tar.gz(r-4.7-any)RFLOMICS_1.5.0.tar.gz(r-4.6-any)
RFLOMICS_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RFLOMICS/json (API)
NEWS

# Install 'RFLOMICS' in R:
install.packages('RFLOMICS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rflomics/rflomics/issues

Datasets:

On BioConductor:RFLOMICS-1.5.0(bioc 3.24)RFLOMICS-1.4.0(bioc 3.23)

shinyappsdifferentialexpressionmetabolomicsproteomicstranscriptomics

6.13 score 60 scripts 246 downloads 83 exports 272 dependencies

Last updated from:f2a9e77256. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE366
linux-devel-x86_64NOTE688
source / vignettesOK529
linux-release-x86_64NOTE776
macos-release-arm64NOTE444
macos-oldrel-arm64NOTE386
windows-develNOTE821
windows-releaseNOTE938
windows-oldrelNOTE905
wasm-releaseOK295

Exports:checkExpDesignCompletenesscreateRflomicsMAEfilterDiffAnalysisgenerateExpressionContrastgenerateModelFormulaegenerateReportgetAnalysisgetAnalyzedDatasetNamesgetAnnotAnalysesSummarygetBatchFactorsgetBioFactorsgetCoeffNormgetCoExpAnalysesSummarygetCoexpClustersgetCoexpSettingsgetDatasetNamesgetDEListgetDEMatrixgetDesignMatgetDiffAnalysesSummarygetDiffSettingsgetDiffStatgetEnrichResgetEnrichSettingsgetFactorModalitiesgetFactorNamesgetFactorTypesgetFilteredFeaturesgetFilterSettingsgetImputSettingsgetMetaFactorsgetMixOmicsgetMixOmicsSettingsgetModelFormulagetMOFAgetMOFASettingsgetNormSettingsgetOmicsTypesgetProcessedDatagetProjectNamegetRflomicsSEgetSelectedContrastsgetSelectedSamplesgetTransSettingsgetValidContrastsisProcessedDataplotBoxplotDEplotClusterProfilerplotCoExpressionplotCoExpressionProfileplotConditionsOverviewplotCoseqContrastsplotDataDistributionplotDataOverviewplotDiffAnalysisplotEnrichCompplotExpDesignCompletenessplotHeatmapDesignplotLibrarySizeplotMissingValuesplotOmicsPCAprepareForIntegrationrflomicsMAE2MAErunAnnotationEnrichmentrunCoExpressionrunDataProcessingrunDiffAnalysisrunFeatureFilteringrunMVImputationrunNormalizationrunOmicsIntegrationrunOmicsPCArunRFLOMICSrunSampleFilteringrunTransformDatasetMixOmicssetModelFormulasetMOFAsetSelectedContrastssetValidContrastssubRflomicsMAEsumMixOmicssumORA

Dependencies:abindaisdkAnnotationDbiapeaplotaskpassbackportsbase64encbasiliskbayesmBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocParallelBiostringsbitbit64blobbootbroombslibcachemcallrcapushecarcarDatacirclizeclasscliclueclusterclusterProfilercodacodetoolscolorspacecommonmarkComplexHeatmapcompositionscorpcorcorrplotcoseqcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDEoptimRDerivDESeq2digestdir.expirydoBydoParallelDOSEdplyrdqrngDTe1071edgeRellipseemmeansenrichitenrichplotestimabilityevaluateFactoMineRfarverfastmapfilelockflashClustFNNfontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesGetoptLongggforceggfunggiraphggnetworkggnewscaleggplot2ggplotifyggpubrggrepelggsciggsignifggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgridExtragridGraphicsgsongtableh5mreadHDF5ArrayherehighrhmshtmltoolshtmlwidgetsHTSClusterHTSFilterhttpuvhttrhttr2igraphIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamixOmicsmodelrMOFA2multcompViewMultiAssayExperimentmvtnormnetworknlmenloptrnnetnumDerivopensslorg.At.tair.dbotelpatchworkpbkrtestpheatmappillarpkgconfigplotlyplotrixplyrpngpolyclippolynomprettyunitsprocessxprogresspromisesproxypspurrrquantregqvalueR6rappdirsrARPACKrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRcppTOMLRdpackreformulasreshape2reticulaterglrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRmixmodrobustbaserprojrootRSpectraRSQLiterstatixRtsneS4ArraysS4VectorsS7sassscalesscatterpiescatterplot3dSeqinfoshapeshinyshinyBSshinydashboardshinyWidgetssitmosnasnowsourcetoolsSparseArraySparseMstatmodstatnet.commonstringistringrSummarizedExperimentsurvivalsyssystemfontstensorAtibbletidydrtidyrtidyselecttidytreetimeDatetinytextreeiotweenrtzdbUpSetRurcautf8uwotvctrsviridisLitevroomwithrxfunxtableXVectoryamlyulab.utilszoo

RFLOMICS

Rendered fromRFLOMICS.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-01-23
Started: 2022-10-17

RFLOMICS Command line

Rendered fromRFLOMICS-command-line.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-04-21
Started: 2024-08-22

RFLOMICS input format

Rendered fromRFLOMICS-input-data.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-01-23
Started: 2022-10-17

Readme and manuals

Help Manual

Help pageTopics
RflomicsMAE class constructorcreateRflomicsMAE
Ecoseed project dataecoseed.df
Ecoseed project dataecoseed.mae
Contrast expressionsgenerateExpressionContrast generateExpressionContrast,RflomicsMAE-method generateExpressionContrast,RflomicsSE-method getSelectedContrasts getSelectedContrasts,RflomicsMAE-method getSelectedContrasts,RflomicsSE-method setSelectedContrasts setSelectedContrasts,RflomicsMAE-method setSelectedContrasts,RflomicsSE-method
Statistical model formulaegenerateModelFormulae generateModelFormulae,RflomicsMAE-method getModelFormula getModelFormula,RflomicsMAE-method getModelFormula,RflomicsSE-method setModelFormula setModelFormula,RflomicsMAE-method setModelFormula,RflomicsSE-method
Generate RFLOMICS html report or archivegenerateReport generateReport,RflomicsMAE-method
Get results from RFLOMICS objectgetAnalysis getAnalysis,RflomicsMAE-method getAnalysis,RflomicsSE-method getAnalyzedDatasetNames getAnalyzedDatasetNames,RflomicsMAE-method
Preparation step for integrationprepareForIntegration prepareForIntegration,RflomicsMAE-method
RflomicsMAE ClassgetBatchFactors getBatchFactors,RflomicsMAE-method getBioFactors getBioFactors,RflomicsMAE-method getDatasetNames getDatasetNames,RflomicsMAE-method getDesignMat getDesignMat,RflomicsMAE-method getFactorModalities getFactorModalities,RflomicsMAE-method getFactorNames getFactorNames,RflomicsMAE-method getFactorTypes getFactorTypes,RflomicsMAE-method getMetaFactors getMetaFactors,RflomicsMAE-method getOmicsTypes getOmicsTypes,RflomicsMAE-method getProjectName getProjectName,RflomicsMAE-method getRflomicsSE getRflomicsSE,RflomicsMAE-method plotConditionsOverview plotConditionsOverview,RflomicsMAE-method plotDataOverview plotDataOverview,RflomicsMAE-method RflomicsMAE-class subRflomicsMAE subRflomicsMAE,RflomicsMAE-method
convert a RflomicsMAE to a MultiAssayExperimentrflomicsMAE2MAE rflomicsMAE2MAE,RflomicsMAE-method
RflomicsSE ClassgetBatchFactors,RflomicsSE-method getBioFactors,RflomicsSE-method getDatasetNames,RflomicsSE-method getDesignMat,RflomicsSE-method getFactorModalities,RflomicsSE-method getFactorNames,RflomicsSE-method getFactorTypes,RflomicsSE-method getMetaFactors,RflomicsSE-method getOmicsTypes,RflomicsSE-method RflomicsSE RflomicsSE-class
Run Gene Enrichment Analysis and process resultsgetAnnotAnalysesSummary getAnnotAnalysesSummary,RflomicsMAE-method getEnrichRes getEnrichRes,RflomicsMAE-method getEnrichRes,RflomicsSE-method getEnrichSettings getEnrichSettings,RflomicsSE-method plotClusterProfiler plotClusterProfiler,RflomicsSE-method plotEnrichComp plotEnrichComp,RflomicsSE-method runAnnotationEnrichment runAnnotationEnrichment,RflomicsMAE-method runAnnotationEnrichment,RflomicsSE-method sumORA sumORA,RflomicsSE-method
Run CoExpression Analysis and process resultsgetCoExpAnalysesSummary getCoExpAnalysesSummary,RflomicsMAE-method getCoexpClusters getCoexpClusters,RflomicsMAE-method getCoexpClusters,RflomicsSE-method getCoexpSettings getCoexpSettings,RflomicsMAE-method getCoexpSettings,RflomicsSE-method plotCoExpression plotCoExpression,RflomicsMAE-method plotCoExpression,RflomicsSE-method plotCoExpressionProfile plotCoExpressionProfile,RflomicsMAE-method plotCoExpressionProfile,RflomicsSE-method plotCoseqContrasts plotCoseqContrasts,RflomicsMAE-method plotCoseqContrasts,RflomicsSE-method runCoExpression runCoExpression,RflomicsMAE-method runCoExpression,RflomicsSE-method
Omic Data Exploratory and PreprocessingcheckExpDesignCompleteness checkExpDesignCompleteness,RflomicsMAE-method checkExpDesignCompleteness,RflomicsSE-method getCoeffNorm getCoeffNorm,RflomicsMAE-method getCoeffNorm,RflomicsSE-method getFilteredFeatures getFilteredFeatures,RflomicsMAE-method getFilteredFeatures,RflomicsSE-method getFilterSettings getFilterSettings,RflomicsMAE-method getFilterSettings,RflomicsSE-method getImputSettings getImputSettings,RflomicsMAE-method getImputSettings,RflomicsSE-method getNormSettings getNormSettings,RflomicsMAE-method getNormSettings,RflomicsSE-method getProcessedData getProcessedData,RflomicsMAE-method getProcessedData,RflomicsSE-method getSelectedSamples getSelectedSamples,RflomicsMAE-method getSelectedSamples,RflomicsSE-method getTransSettings getTransSettings,RflomicsMAE-method getTransSettings,RflomicsSE-method isProcessedData isProcessedData,RflomicsMAE-method isProcessedData,RflomicsSE-method plotDataDistribution plotDataDistribution,RflomicsMAE-method plotDataDistribution,RflomicsSE-method plotExpDesignCompleteness plotExpDesignCompleteness,RflomicsMAE-method plotExpDesignCompleteness,RflomicsSE-method plotLibrarySize plotLibrarySize,RflomicsMAE-method plotLibrarySize,RflomicsSE-method plotMissingValues plotMissingValues,RflomicsMAE-method plotMissingValues,RflomicsSE-method plotOmicsPCA plotOmicsPCA,RflomicsMAE-method plotOmicsPCA,RflomicsSE-method runDataProcessing runDataProcessing,RflomicsMAE-method runDataProcessing,RflomicsSE-method runFeatureFiltering runFeatureFiltering,RflomicsMAE-method runFeatureFiltering,RflomicsSE-method runMVImputation runMVImputation,RflomicsMAE-method runMVImputation,RflomicsSE-method runNormalization runNormalization,RflomicsMAE-method runNormalization,RflomicsSE-method runOmicsPCA runOmicsPCA,RflomicsMAE-method runOmicsPCA,RflomicsSE-method runSampleFiltering runSampleFiltering,RflomicsMAE-method runSampleFiltering,RflomicsSE-method runTransformData runTransformData,RflomicsMAE-method runTransformData,RflomicsSE-method
Run Differential Expression Analysis and process resultsfilterDiffAnalysis filterDiffAnalysis,RflomicsMAE-method filterDiffAnalysis,RflomicsSE-method getDEList getDEList,RflomicsMAE-method getDEList,RflomicsSE-method getDEMatrix getDEMatrix,RflomicsMAE-method getDEMatrix,RflomicsSE-method getDiffAnalysesSummary getDiffAnalysesSummary,RflomicsMAE-method getDiffSettings getDiffSettings,RflomicsMAE-method getDiffSettings,RflomicsSE-method getDiffStat getDiffStat,RflomicsMAE-method getDiffStat,RflomicsSE-method getValidContrasts getValidContrasts,RflomicsMAE-method getValidContrasts,RflomicsSE-method plotBoxplotDE plotBoxplotDE,RflomicsMAE-method plotBoxplotDE,RflomicsSE-method plotDiffAnalysis plotDiffAnalysis,RflomicsMAE-method plotDiffAnalysis,RflomicsSE-method plotHeatmapDesign plotHeatmapDesign,RflomicsMAE-method plotHeatmapDesign,RflomicsSE-method runDiffAnalysis runDiffAnalysis,RflomicsMAE-method runDiffAnalysis,RflomicsSE-method setValidContrasts setValidContrasts,RflomicsMAE-method setValidContrasts,RflomicsSE-method
runOmicsIntegrationgetMixOmics getMixOmics,RflomicsMAE-method getMixOmicsSettings getMixOmicsSettings,RflomicsMAE-method getMOFA getMOFA,RflomicsMAE-method getMOFASettings getMOFASettings,RflomicsMAE-method runOmicsIntegration runOmicsIntegration,RflomicsMAE-method setMixOmics setMixOmics,RflomicsMAE-method setMOFA setMOFA,RflomicsMAE-method sumMixOmics sumMixOmics,RflomicsMAE-method
Run RFLOMICS interfacerunRFLOMICS