Package: debrowser 1.35.0

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:Alper Kucukural <[email protected]>, Onur Yukselen <[email protected]>, Manuel Garber <[email protected]>

debrowser_1.35.0.tar.gz
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debrowser.pdf |debrowser.html✨
debrowser/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/umms-biocore/debrowser/issues

On BioConductor:debrowser-1.35.0(bioc 3.21)debrowser-1.34.0(bioc 3.20)

sequencingchipseqrnaseqdifferentialexpressiongeneexpressionclusteringimmunooncology

8.08 score 60 stars 63 scripts 345 downloads 2 mentions 191 exports 215 dependencies

Last updated 2 months agofrom:d89617313a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:actionButtonDEaddDataColsaddIDall2allall2allControlsUIapplyFiltersapplyFiltersNewapplyFiltersToMergedComparisonbarMainPlotControlsUIbatchEffectUIbatchMethodBoxMainPlotControlsUIchangeClusterOrdercheckCountDatacheckMetaDataclusterDataclustFunParamsUIcompareClustcondSelectUIcorrectCombatcorrectHarmancustomColorsUIcutOffSelectionUIdataLCFUIdataLoadUIdebrowserall2alldebrowserbarmainplotdebrowserbatcheffectdebrowserboxmainplotdebrowsercondselectdebrowserdataloaddebrowserdeanalysisdebrowserdensityplotdebrowserheatmapdebrowserhistogramdebrowserIQRplotdebrowserlowcountfilterdebrowsermainplotdebrowserpcaplotdendControlsUIdensityPlotControlsUIdeServerdeUIdistFunParamsUIdrawKEGGdrawPCAExplainedfileTypesfileUploadBoxgenerateTestDataget_conditions_given_selectiongetAfterLoadMsggetAll2AllPlotUIgetBarMainPlotgetBarMainPlotUIgetBoxMainPlotgetBoxMainPlotUIgetBSTableUIgetColorsgetColorShapeSelectiongetCompSelectiongetConditionSelectorgetConditionSelectorFromMetagetCondMsggetCovariateDetailsgetCutOffSelectiongetDataAssesmentTextgetDataForTablesgetDataPreparationTextgetDEAnalysisTextgetDensityPlotgetDensityPlotUIgetDEResultsUIgetDomainsgetDowngetDownloadSectiongetEnrichDOgetEnrichGOgetEnrichKEGGgetEntrezIdsgetEntrezTablegetGeneListgetGeneSetDatagetGOLeftMenugetGoPanelgetGOPlotsgetGroupSelectorgetGSEAgetHeatmapUIgetHelpButtongetHideLegendOnOffgetHistogramUIgetIntroTextgetIQRPlotgetIQRPlotUIgetJSLinegetKEGGModalgetLeftMenugetLegendColorsgetLegendRadiogetLegendSelectgetLevelOrdergetLoadingMsggetLogogetMainPanelgetMainPlotsLeftMenugetMainPlotUIgetMeangetMergedComparisongetMetaSelectorgetMethodDetailsgetMostVariedListgetNormalizedMatrixgetOrganismgetOrganismBoxgetOrganismPathwaygetPCAcontolUpdatesJSgetPCAexplainedgetPCAPlotUIgetPCselectiongetPlotAreagetProgramTitlegetQATextgetQCLeftMenugetQCPanelgetSampleDetailsgetSampleNamesgetSearchDatagetSelectedColsgetSelectedDatasetInputgetSelectInputBoxgetSelHeatgetShapeColorgetStartPlotsMsggetStartupMsggetTableDetailsgetTableModalgetTableStylegetTabUpdateJSgetUpgetUpDowngetVariationDataheatmapControlsUIheatmapJScodeheatmapServerheatmapUIhideObjhistogramControlsUIinstallpackIQRPlotControlsUIkmeansControlsUIlcfMetRadioloadpackmainPlotControlsUImainScatterNewniceKmeansnormalizationMethodspalUIpanel.corpanel.histpcaPlotControlsUIplot_pcaplotDataplotMarginsUIplotSizeMarginsUIplotSizeUIplotTypeUIprepDataContainerprepGroupprepHeatDataprepPCADatpushremoveColsremoveExtraColsround_valsrun_pcarunDErunDESeq2runEdgeRrunHeatmaprunHeatmap2runLimmaselectConditionsselectedInputselectGroupInfosepRadiosetBatchshowObjstartDEBrowserstartHeatmaptextareaInputtogglePanels

Dependencies:abindannotateAnnotationDbiapeapeglmaplotashraskpassassertthatbase64encbbmlebdsmatrixBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbslibcacachemcallrcaToolsCkmeans.1d.dpcliclusterclusterProfilercodacodetoolscolorspacecolourpickercommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydendextendDESeq2digestDOSEdplyrDTedgeReggemdbookenrichplotetrunctevaluatefansifarverfastmapfastmatchfgseafontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgplotsgraphgridExtragridGraphicsgsongtablegtoolsHarmanheatmaplyhighrhtmltoolshtmlwidgetshttpuvhttrigraphinvgammaIRangesirlbaisobanditeratorsjquerylibjsonliteKEGGgraphKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImixsqpmunsellmvtnormnlmenumDerivopensslorg.Hs.eg.dborg.Mm.eg.dbpatchworkpathviewpermutepillarpkgconfigplogrplotlyplyrpngpolyclipprocessxpromisespspurrrqapqvalueR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlRdpackregistryreshape2RgraphvizrlangrmarkdownRSQLiteS4ArraysS4VectorssassscalesscatterpieseriationshinyshinyBSshinydashboardshinyjssnowsourcetoolsSparseArraySQUAREMstatmodstringistringrSummarizedExperimentsurvivalsvasyssystemfontstibbletidyrtidyselecttidytreetinytextreeiotruncnormTSPtweenrUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc

DEBrowser user guide

Alper Kucukural, Onur Yukselen, Manuel Garber

Rendered fromDEBrowser.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-06-01
Started: 2016-03-23

Readme and manuals

Help Manual

Help pageTopics
Buttons including Action Buttons and Event ButtonsactionButtonDE
addDataColsaddDataCols
addIDaddID
all2allall2all
all2allControlsUIall2allControlsUI
applyFiltersapplyFilters
applyFiltersNewapplyFiltersNew
applyFiltersToMergedComparisonapplyFiltersToMergedComparison
barMainPlotControlsUIbarMainPlotControlsUI
batchEffectUI Creates a panel to coorect batch effectbatchEffectUI
batchMethodbatchMethod
BoxMainPlotControlsUIBoxMainPlotControlsUI
changeClusterOrderchangeClusterOrder
checkCountDatacheckCountData
checkMetaDatacheckMetaData
clusterDataclusterData
clustFunParamsUIclustFunParamsUI
compareClustcompareClust
condSelectUI Creates a panel to select samples for each conditioncondSelectUI
Correct Batch Effect using Combat in sva packagecorrectCombat
Correct Batch Effect using HarmancorrectHarman
customColorsUIcustomColorsUI
cutOffSelectionUIcutOffSelectionUI
dataLCFUI Creates a panel to filter low count genes and regionsdataLCFUI
dataLoadUIdataLoadUI
debrowserall2alldebrowserall2all
debrowserbarmainplotdebrowserbarmainplot
debrowserbatcheffectdebrowserbatcheffect
debrowserboxmainplotdebrowserboxmainplot
debrowsercondselectdebrowsercondselect
debrowserdataloaddebrowserdataload
debrowserdeanalysisdebrowserdeanalysis
debrowserdensityplotdebrowserdensityplot
debrowserheatmapdebrowserheatmap
debrowserhistogramdebrowserhistogram
debrowserIQRplotdebrowserIQRplot
debrowserlowcountfilterdebrowserlowcountfilter
debrowsermainplotdebrowsermainplot
debrowserpcaplotdebrowserpcaplot
dendControlsUIdendControlsUI
densityPlotControlsUIdensityPlotControlsUI
deServerdeServer
deUIdeUI
distFunParamsUIdistFunParamsUI
drawKEGGdrawKEGG
Creates a more detailed plot using the PCA results from the selected dataset.drawPCAExplained
fileTypesfileTypes
fileUploadBoxfileUploadBox
generateTestDatagenerateTestData
get_conditions_given_selectionget_conditions_given_selection
getAfterLoadMsggetAfterLoadMsg
getAll2AllPlotUIgetAll2AllPlotUI
getBarMainPlotgetBarMainPlot
getBarMainPlotUIgetBarMainPlotUI
getBoxMainPlotgetBoxMainPlot
getBoxMainPlotUIgetBoxMainPlotUI
getBSTableUI prepares a Modal to put a tablegetBSTableUI
getColorsgetColors
getColorShapeSelectiongetColorShapeSelection
getCompSelectiongetCompSelection
getConditionSelectorgetConditionSelector
getConditionSelectorFromMetagetConditionSelectorFromMeta
getCondMsggetCondMsg
getCovariateDetailsgetCovariateDetails
getCutOffSelectiongetCutOffSelection
getDataAssesmentText DataAssesment textgetDataAssesmentText
getDataForTables get data to fill up tables tabgetDataForTables
getDataPreparationText DataPreparation textgetDataPreparationText
getDEAnalysisText DEAnalysis textgetDEAnalysisText
getDensityPlotgetDensityPlot
getDensityPlotUIgetDensityPlotUI
getDEResultsUI Creates a panel to visualize DE resultsgetDEResultsUI
getDomainsgetDomains
getDown get down regulated datagetDown
getDownloadSectiongetDownloadSection
getEnrichDOgetEnrichDO
getEnrichGOgetEnrichGO
getEnrichKEGGgetEnrichKEGG
getEntrezIdsgetEntrezIds
getEntrezTablegetEntrezTable
getGeneListgetGeneList
getGeneSetDatagetGeneSetData
getGOLeftMenugetGOLeftMenu
getGoPanelgetGoPanel
getGOPlotsgetGOPlots
getGroupSelector Return the groupsgetGroupSelector
getGSEAgetGSEA
getHeatmapUIgetHeatmapUI
getHelpButton prepares a helpbutton for to go to a specific site in the documentationgetHelpButton
getHideLegendOnOffgetHideLegendOnOff
getHistogramUIgetHistogramUI
getIntroText Intro textgetIntroText
getIQRPlotgetIQRPlot
getIQRPlotUIgetIQRPlotUI
getJSLinegetJSLine
getKEGGModal prepares a modal for KEGG plotsgetKEGGModal
getLeftMenugetLeftMenu
getLegendColorsgetLegendColors
getLegendRadiogetLegendRadio
getLegendSelectgetLegendSelect
getLevelOrdergetLevelOrder
getLoadingMsggetLoadingMsg
getLogogetLogo
getMainPanelgetMainPanel
getMainPlotsLeftMenugetMainPlotsLeftMenu
getMainPlotUIgetMainPlotUI
getMeangetMean
getMergedComparisongetMergedComparison
getMetaSelectorgetMetaSelector
get the detail boxes after DE method selectedgetMethodDetails
getMostVariedListgetMostVariedList
getNormalizedMatrixgetNormalizedMatrix
getOrganismgetOrganism
getOrganismBoxgetOrganismBox
getOrganismPathwaygetOrganismPathway
getPCAcontolUpdatesJS in the prep menu we have two PCA plots to show how batch effect correction worked. One set of PCA input controls updates two PCA plots with this JS.getPCAcontolUpdatesJS
getPCAexplainedgetPCAexplained
getPCAPlotUIgetPCAPlotUI
getPCselectiongetPCselection
getPlotAreagetPlotArea
getProgramTitlegetProgramTitle
getQAText Some questions and answersgetQAText
getQCLeftMenugetQCLeftMenu
getQCPanelgetQCPanel
getSampleDetailsgetSampleDetails
getSampleNamesgetSampleNames
getSearchDatagetSearchData
getSelectedColsgetSelectedCols
getSelectedDatasetInputgetSelectedDatasetInput
getSelectInputBoxgetSelectInputBox
getSelHeatgetSelHeat
getShapeColorgetShapeColor
getStartPlotsMsggetStartPlotsMsg
getStartupMsggetStartupMsg
getTableDetailsgetTableDetails
getTableModal prepares table modal for KEGGgetTableModal
getTableStylegetTableStyle
getTabUpdateJS prepmenu tab and discovery menu tab updatesgetTabUpdateJS
getUp get up regulated datagetUp
getUpDown get up+down regulated datagetUpDown
getVariationDatagetVariationData
heatmapControlsUIheatmapControlsUI
heatmapJScodeheatmapJScode
heatmapServerheatmapServer
heatmapUIheatmapUI
hideObjhideObj
histogramControlsUIhistogramControlsUI
installpackinstallpack
IQRPlotControlsUIIQRPlotControlsUI
kmeansControlsUIkmeansControlsUI
lcfMetRadiolcfMetRadio
loadpackloadpack
mainPlotControlsUImainPlotControlsUI
mainScatterNewmainScatterNew
niceKmeansniceKmeans
normalizationMethodsnormalizationMethods
palUIpalUI
panel.corpanel.cor
panel.histpanel.hist
pcaPlotControlsUIpcaPlotControlsUI
plot_pcaplot_pca
plotDataplotData
plotMarginsUIplotMarginsUI
plotSizeMarginsUIplotSizeMarginsUI
plotSizeUIplotSizeUI
plotTypeUIplotTypeUI
prepDataContainerprepDataContainer
prepGroupprepGroup
prepHeatDataprepHeatData
prepPCADatprepPCADat
pushpush
removeColsremoveCols
removeExtraColsremoveExtraCols
round_valsround_vals
run_pcarun_pca
runDErunDE
runDESeq2runDESeq2
runEdgeRrunEdgeR
runHeatmaprunHeatmap
runHeatmap2runHeatmap2
runLimmarunLimma
selectConditionsselectConditions
selectedInputselectedInput
selectGroupInfoselectGroupInfo
sepRadiosepRadio
setBatch to skip batch effect correction batch variable set with the filter resultssetBatch
showObjshowObj
startDEBrowserstartDEBrowser
startHeatmapstartHeatmap
textareaInputtextareaInput
togglePanelstogglePanels