# Interactive Differential Expresion Analysis Browser

## Documentation for package ‘debrowser’ version 1.39.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D F G H I K L M N P R S T

## -- A --

actionButtonDE | Buttons including Action Buttons and Event Buttons
addDataCols | addDataCols
addID | addID
all2all | all2all
all2allControlsUI | all2allControlsUI
applyFilters | applyFilters
applyFiltersNew | applyFiltersNew
applyFiltersToMergedComparison | applyFiltersToMergedComparison

## -- B --

barMainPlotControlsUI | barMainPlotControlsUI
batchEffectUI | batchEffectUI Creates a panel to coorect batch effect
batchMethod | batchMethod
BoxMainPlotControlsUI | BoxMainPlotControlsUI

## -- C --

changeClusterOrder | changeClusterOrder
checkCountData | checkCountData
checkMetaData | checkMetaData
clusterData | clusterData
clustFunParamsUI | clustFunParamsUI
compareClust | compareClust
condSelectUI | condSelectUI Creates a panel to select samples for each condition
correctCombat | Correct Batch Effect using Combat in sva package
correctHarman | Correct Batch Effect using Harman
customColorsUI | customColorsUI
cutOffSelectionUI | cutOffSelectionUI

## -- D --

dataLCFUI | dataLCFUI Creates a panel to filter low count genes and regions
dataLoadUI | dataLoadUI
debrowserall2all | debrowserall2all
debrowserbarmainplot | debrowserbarmainplot
debrowserbatcheffect | debrowserbatcheffect
debrowserboxmainplot | debrowserboxmainplot
debrowsercondselect | debrowsercondselect
debrowserdataload | debrowserdataload
debrowserdeanalysis | debrowserdeanalysis
debrowserdensityplot | debrowserdensityplot
debrowserheatmap | debrowserheatmap
debrowserhistogram | debrowserhistogram
debrowserIQRplot | debrowserIQRplot
debrowserlowcountfilter | debrowserlowcountfilter
debrowsermainplot | debrowsermainplot
debrowserpcaplot | debrowserpcaplot
dendControlsUI | dendControlsUI
densityPlotControlsUI | densityPlotControlsUI
deServer | deServer
deUI | deUI
distFunParamsUI | distFunParamsUI
drawKEGG | drawKEGG
drawPCAExplained | Creates a more detailed plot using the PCA results from the selected dataset.

## -- F --

fileTypes | fileTypes
fileUploadBox | fileUploadBox

## -- G --

generateTestData | generateTestData
getAfterLoadMsg | getAfterLoadMsg
getAll2AllPlotUI | getAll2AllPlotUI
getBarMainPlot | getBarMainPlot
getBarMainPlotUI | getBarMainPlotUI
getBoxMainPlot | getBoxMainPlot
getBoxMainPlotUI | getBoxMainPlotUI
getBSTableUI | getBSTableUI prepares a Modal to put a table
getColors | getColors
getColorShapeSelection | getColorShapeSelection
getCompSelection | getCompSelection
getConditionSelector | getConditionSelector
getConditionSelectorFromMeta | getConditionSelectorFromMeta
getCondMsg | getCondMsg
getCovariateDetails | getCovariateDetails
getCutOffSelection | getCutOffSelection
getDataAssesmentText | getDataAssesmentText DataAssesment text
getDataForTables | getDataForTables get data to fill up tables tab
getDataPreparationText | getDataPreparationText DataPreparation text
getDEAnalysisText | getDEAnalysisText DEAnalysis text
getDensityPlot | getDensityPlot
getDensityPlotUI | getDensityPlotUI
getDEResultsUI | getDEResultsUI Creates a panel to visualize DE results
getDomains | getDomains
getDown | getDown get down regulated data
getDownloadSection | getDownloadSection
getEnrichDO | getEnrichDO
getEnrichGO | getEnrichGO
getEnrichKEGG | getEnrichKEGG
getEntrezIds | getEntrezIds
getEntrezTable | getEntrezTable
getGeneList | getGeneList
getGeneSetData | getGeneSetData
getGOLeftMenu | getGOLeftMenu
getGoPanel | getGoPanel
getGOPlots | getGOPlots
getGroupSelector | getGroupSelector Return the groups
getGSEA | getGSEA
getHeatmapUI | getHeatmapUI
getHelpButton | getHelpButton prepares a helpbutton for to go to a specific site in the documentation
getHideLegendOnOff | getHideLegendOnOff
getHistogramUI | getHistogramUI
getIntroText | getIntroText Intro text
getIQRPlot | getIQRPlot
getIQRPlotUI | getIQRPlotUI
getJSLine | getJSLine
getKEGGModal | getKEGGModal prepares a modal for KEGG plots
getLeftMenu | getLeftMenu
getLegendColors | getLegendColors
getLegendRadio | getLegendRadio
getLegendSelect | getLegendSelect
getLevelOrder | getLevelOrder
getLoadingMsg | getLoadingMsg
getLogo | getLogo
getMainPanel | getMainPanel
getMainPlotsLeftMenu | getMainPlotsLeftMenu
getMainPlotUI | getMainPlotUI
getMean | getMean
getMergedComparison | getMergedComparison
getMetaSelector | getMetaSelector
getMethodDetails | get the detail boxes after DE method selected
getMostVariedList | getMostVariedList
getNormalizedMatrix | getNormalizedMatrix
getOrganism | getOrganism
getOrganismBox | getOrganismBox
getOrganismPathway | getOrganismPathway
getPCAcontolUpdatesJS | 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.
getPCAexplained | getPCAexplained
getPCAPlotUI | getPCAPlotUI
getPCselection | getPCselection
getPlotArea | getPlotArea
getProgramTitle | getProgramTitle
getQAText | getQAText Some questions and answers
getQCLeftMenu | getQCLeftMenu
getQCPanel | getQCPanel
getSampleDetails | getSampleDetails
getSampleNames | getSampleNames
getSearchData | getSearchData
getSelectedCols | getSelectedCols
getSelectedDatasetInput | getSelectedDatasetInput
getSelectInputBox | getSelectInputBox
getSelHeat | getSelHeat
getShapeColor | getShapeColor
getStartPlotsMsg | getStartPlotsMsg
getStartupMsg | getStartupMsg
getTableDetails | getTableDetails
getTableModal | getTableModal prepares table modal for KEGG
getTableStyle | getTableStyle
getTabUpdateJS | getTabUpdateJS prepmenu tab and discovery menu tab updates
getUp | getUp get up regulated data
getUpDown | getUpDown get up+down regulated data
getVariationData | getVariationData
get_conditions_given_selection | get_conditions_given_selection

## -- H --

heatmapControlsUI | heatmapControlsUI
heatmapJScode | heatmapJScode
heatmapServer | heatmapServer
heatmapUI | heatmapUI
hideObj | hideObj
histogramControlsUI | histogramControlsUI

## -- I --

installpack | installpack
IQRPlotControlsUI | IQRPlotControlsUI

## -- K --

kmeansControlsUI | kmeansControlsUI

## -- L --

lcfMetRadio | lcfMetRadio
loadpack | loadpack

## -- M --

mainPlotControlsUI | mainPlotControlsUI
mainScatterNew | mainScatterNew

## -- N --

niceKmeans | niceKmeans
normalizationMethods | normalizationMethods

## -- P --

palUI | palUI
panel.cor | panel.cor
panel.hist | panel.hist
pcaPlotControlsUI | pcaPlotControlsUI
plotData | plotData
plotMarginsUI | plotMarginsUI
plotSizeMarginsUI | plotSizeMarginsUI
plotSizeUI | plotSizeUI
plotTypeUI | plotTypeUI
plot_pca | plot_pca
prepDataContainer | prepDataContainer
prepGroup | prepGroup
prepHeatData | prepHeatData
prepPCADat | prepPCADat
push | push

## -- R --

removeCols | removeCols
removeExtraCols | removeExtraCols
round_vals | round_vals
runDE | runDE
runDESeq2 | runDESeq2
runEdgeR | runEdgeR
runHeatmap | runHeatmap
runHeatmap2 | runHeatmap2
runLimma | runLimma
run_pca | run_pca

## -- S --

selectConditions | selectConditions
selectedInput | selectedInput
selectGroupInfo | selectGroupInfo
sepRadio | sepRadio
setBatch | setBatch to skip batch effect correction batch variable set with the filter results
showObj | showObj
startDEBrowser | startDEBrowser
startHeatmap | startHeatmap

## -- T --

textareaInput | textareaInput
togglePanels | togglePanels