DEBrowser: | Introduction | DEBrowser | Quick start | Browsing your Data | Data via TSV file | Low Count Filtering | Batch Effect Corrections | DE Analysis: | The Main Plots of DE Analysis: | Differential Expression Calculations | DESeq2 | Un-normalized counts | Used parameters for DESeq2 | EdgeR | Used parameters for EdgeR | Limma | Used parameters for Limma | The Heatmap of DE Analysis | Used clustering and linkage methods in heatmap | Used distance methods in heatmap | Interactive Heatmap | The Scale Option of Heatmap | GO Term Plots | Data Tables | Quality Control Plots | Examples | QC plots without Batch Effect Correction | QC plots after Batch Effect Correction | The Differential Expression Plots | Log2 fold change comparison for PPARα pathway | Case Study | Operating System Dependencies | Autoload Data via Hyperlink | References
Package: debrowser 1.41.0
Alper Kucukural
debrowser: Interactive Differential Expresion Analysis Browser
Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.
Authors:
debrowser_1.41.0.tar.gz
debrowser_1.41.0.zip(r-4.7)debrowser_1.41.0.zip(r-4.6)debrowser_1.41.0.zip(r-4.5)
debrowser_1.41.0.tgz(r-4.6-any)debrowser_1.41.0.tgz(r-4.5-any)
debrowser_1.41.0.tar.gz(r-4.7-any)debrowser_1.41.0.tar.gz(r-4.6-any)
debrowser_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
debrowser/json (API)
| # Install 'debrowser' in R: |
| install.packages('debrowser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/umms-biocore/debrowser/issues
On BioConductor:debrowser-1.41.0(bioc 3.24)debrowser-1.40.0(bioc 3.23)
sequencingchipseqrnaseqdifferentialexpressiongeneexpressionclusteringimmunooncology
Last updated from:62ff5f1ce9. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 296 | ||
| linux-devel-x86_64 | NOTE | 579 | ||
| source / vignettes | OK | 391 | ||
| linux-release-x86_64 | NOTE | 557 | ||
| macos-release-arm64 | NOTE | 290 | ||
| macos-oldrel-arm64 | NOTE | 286 | ||
| windows-devel | NOTE | 408 | ||
| windows-release | NOTE | 444 | ||
| windows-oldrel | NOTE | 458 | ||
| wasm-release | OK | 279 |
Exports:actionButtonDEaddDataColsaddIDall2allall2allControlsUIapplyFiltersapplyFiltersNewapplyFiltersToMergedComparisonbarMainPlotControlsUIbatchEffectUIbatchMethodBoxMainPlotControlsUIchangeClusterOrdercheckCountDatacheckMetaDataclusterDataclustFunParamsUIcompareClustcondSelectUIcorrectCombatcorrectHarmancustomColorsUIcutOffSelectionUIdataLCFUIdataLoadUIdebrowserall2alldebrowserbarmainplotdebrowserbatcheffectdebrowserboxmainplotdebrowsercondselectdebrowserdataloaddebrowserdeanalysisdebrowserdensityplotdebrowserheatmapdebrowserhistogramdebrowserIQRplotdebrowserlowcountfilterdebrowsermainplotdebrowserpcaplotdendControlsUIdensityPlotControlsUIdeServerdeUIdistFunParamsUIdrawKEGGdrawPCAExplainedfileTypesfileUploadBoxgenerateTestDataget_conditions_given_selectiongetAfterLoadMsggetAll2AllPlotUIgetBarMainPlotgetBarMainPlotUIgetBoxMainPlotgetBoxMainPlotUIgetBSTableUIgetColorsgetColorShapeSelectiongetCompSelectiongetConditionSelectorgetConditionSelectorFromMetagetCondMsggetCovariateDetailsgetCutOffSelectiongetDataAssesmentTextgetDataForTablesgetDataPreparationTextgetDEAnalysisTextgetDensityPlotgetDensityPlotUIgetDEResultsUIgetDomainsgetDowngetDownloadSectiongetEnrichDOgetEnrichGOgetEnrichKEGGgetEntrezIdsgetEntrezTablegetGeneListgetGeneSetDatagetGOLeftMenugetGoPanelgetGOPlotsgetGroupSelectorgetGSEAgetHeatmapUIgetHelpButtongetHideLegendOnOffgetHistogramUIgetIntroTextgetIQRPlotgetIQRPlotUIgetJSLinegetKEGGModalgetLeftMenugetLegendColorsgetLegendRadiogetLegendSelectgetLevelOrdergetLoadingMsggetLogogetMainPanelgetMainPlotsLeftMenugetMainPlotUIgetMeangetMergedComparisongetMetaSelectorgetMethodDetailsgetMostVariedListgetNormalizedMatrixgetOrganismgetOrganismBoxgetOrganismPathwaygetPCAcontolUpdatesJSgetPCAexplainedgetPCAPlotUIgetPCselectiongetPlotAreagetProgramTitlegetQATextgetQCLeftMenugetQCPanelgetSampleDetailsgetSampleNamesgetSearchDatagetSelectedColsgetSelectedDatasetInputgetSelectInputBoxgetSelHeatgetShapeColorgetStartPlotsMsggetStartupMsggetTableDetailsgetTableModalgetTableStylegetTabUpdateJSgetUpgetUpDowngetVariationDataheatmapControlsUIheatmapJScodeheatmapServerheatmapUIhideObjhistogramControlsUIinstallpackIQRPlotControlsUIkmeansControlsUIlcfMetRadioloadpackmainPlotControlsUImainScatterNewniceKmeansnormalizationMethodspalUIpanel.corpanel.histpcaPlotControlsUIplot_pcaplotDataplotMarginsUIplotSizeMarginsUIplotSizeUIplotTypeUIprepDataContainerprepGroupprepHeatDataprepPCADatpushremoveColsremoveExtraColsround_valsrun_pcarunDErunDESeq2runEdgeRrunHeatmaprunHeatmap2runLimmaselectConditionsselectedInputselectGroupInfosepRadiosetBatchshowObjstartDEBrowserstartHeatmaptextareaInputtogglePanels
Dependencies:abindaisdkannotateAnnotationDbiapeapeglmaplotashraskpassassertthatbase64encbbmlebdsmatrixBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbslibcacachemcallrcaToolsCkmeans.1d.dpcliclusterclusterProfilercodacodetoolscolorspacecolourpickercommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydendextendDESeq2digestDOSEdplyrDTedgeReggemdbookenrichitenrichplotetrunctevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgclusgdtoolsgenefiltergenericsGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgplotsgraphgridExtragridGraphicsgsongtablegtoolsHarmanheatmaplyhighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphinvgammaIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGgraphKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImixsqpmvtnormnlmenumDerivopensslorg.Hs.eg.dborg.Mm.eg.dbotelpatchworkpathviewpermutepillarpkgconfigplotlyplyrpngpolyclipprocessxpromisespspurrrqapqvalueR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlRdpackregistryreshape2RgraphvizrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesscatterpieSeqinfoseriationshinyshinyBSshinydashboardshinyjssnowsourcetoolsSparseArraySQUAREMstatmodstringistringrSummarizedExperimentsurvivalsvasyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotruncnormTSPtweenrutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxtableXVectoryamlyulab.utils
