BoxMainPlotControlsUI   BoxMainPlotControlsUI
IQRPlotControlsUI       IQRPlotControlsUI
actionButtonDE          Buttons including Action Buttons and Event
                        Buttons
addDataCols             addDataCols
addID                   addID
all2all                 all2all
all2allControlsUI       all2allControlsUI
applyFilters            applyFilters
applyFiltersNew         applyFiltersNew
applyFiltersToMergedComparison
                        applyFiltersToMergedComparison
barMainPlotControlsUI   barMainPlotControlsUI
batchEffectUI           batchEffectUI Creates a panel to coorect batch
                        effect
batchMethod             batchMethod
changeClusterOrder      changeClusterOrder
checkCountData          checkCountData
checkMetaData           checkMetaData
clustFunParamsUI        clustFunParamsUI
clusterData             clusterData
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
dataLCFUI               dataLCFUI Creates a panel to filter low count
                        genes and regions
dataLoadUI              dataLoadUI
deServer                deServer
deUI                    deUI
debrowserIQRplot        debrowserIQRplot
debrowserall2all        debrowserall2all
debrowserbarmainplot    debrowserbarmainplot
debrowserbatcheffect    debrowserbatcheffect
debrowserboxmainplot    debrowserboxmainplot
debrowsercondselect     debrowsercondselect
debrowserdataload       debrowserdataload
debrowserdeanalysis     debrowserdeanalysis
debrowserdensityplot    debrowserdensityplot
debrowserheatmap        debrowserheatmap
debrowserhistogram      debrowserhistogram
debrowserlowcountfilter
                        debrowserlowcountfilter
debrowsermainplot       debrowsermainplot
debrowserpcaplot        debrowserpcaplot
dendControlsUI          dendControlsUI
densityPlotControlsUI   densityPlotControlsUI
distFunParamsUI         distFunParamsUI
drawKEGG                drawKEGG
drawPCAExplained        Creates a more detailed plot using the PCA
                        results from the selected dataset.
fileTypes               fileTypes
fileUploadBox           fileUploadBox
generateTestData        generateTestData
getAfterLoadMsg         getAfterLoadMsg
getAll2AllPlotUI        getAll2AllPlotUI
getBSTableUI            getBSTableUI prepares a Modal to put a table
getBarMainPlot          getBarMainPlot
getBarMainPlotUI        getBarMainPlotUI
getBoxMainPlot          getBoxMainPlot
getBoxMainPlotUI        getBoxMainPlotUI
getColorShapeSelection
                        getColorShapeSelection
getColors               getColors
getCompSelection        getCompSelection
getCondMsg              getCondMsg
getConditionSelector    getConditionSelector
getConditionSelectorFromMeta
                        getConditionSelectorFromMeta
getCutOffSelection      getCutOffSelection
getDEAnalysisText       getDEAnalysisText DEAnalysis text
getDEResultsUI          getDEResultsUI Creates a panel to visualize DE
                        results
getDataAssesmentText    getDataAssesmentText DataAssesment text
getDataForTables        getDataForTables get data to fill up tables tab
getDataPreparationText
                        getDataPreparationText DataPreparation text
getDensityPlot          getDensityPlot
getDensityPlotUI        getDensityPlotUI
getDomains              getDomains
getDown                 getDown get down regulated data
getDownloadSection      getDownloadSection
getEnrichDO             getEnrichDO
getEnrichGO             getEnrichGO
getEnrichKEGG           getEnrichKEGG
getEntrezIds            getEntrezIds
getEntrezTable          getEntrezTable
getGOLeftMenu           getGOLeftMenu
getGOPlots              getGOPlots
getGSEA                 getGSEA
getGeneList             getGeneList
getGeneSetData          getGeneSetData
getGoPanel              getGoPanel
getHeatmapUI            getHeatmapUI
getHelpButton           getHelpButton prepares a helpbutton for to go
                        to a specific site in the documentation
getHideLegendOnOff      getHideLegendOnOff
getHistogramUI          getHistogramUI
getIQRPlot              getIQRPlot
getIQRPlotUI            getIQRPlotUI
getIntroText            getIntroText Intro text
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
getMainPlotUI           getMainPlotUI
getMainPlotsLeftMenu    getMainPlotsLeftMenu
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
getPCAPlotUI            getPCAPlotUI
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
getPCselection          getPCselection
getPlotArea             getPlotArea
getProgramTitle         getProgramTitle
getQAText               getQAText Some questions and answers
getQCLeftMenu           getQCLeftMenu
getQCPanel              getQCPanel
getSampleDetails        getSampleDetails
getSampleNames          getSampleNames
getSamples              getSamples
getSearchData           getSearchData
getSelHeat              getSelHeat
getSelectInputBox       getSelectInputBox
getSelectedCols         getSelectedCols
getSelectedDatasetInput
                        getSelectedDatasetInput
getShapeColor           getShapeColor
getStartPlotsMsg        getStartPlotsMsg
getStartupMsg           getStartupMsg
getTabUpdateJS          getTabUpdateJS prepmenu tab and discovery menu
                        tab updates
getTableDetails         getTableDetails
getTableModal           getTableModal prepares table modal for KEGG
getTableStyle           getTableStyle
getTextOnOff            getTextOnOff
getUp                   getUp get up regulated data
getUpDown               getUpDown get up+down regulated data
getVariationData        getVariationData
get_conditions_given_selection
                        get_conditions_given_selection
heatmapControlsUI       heatmapControlsUI
heatmapJScode           heatmapJScode
heatmapServer           heatmapServer
heatmapUI               heatmapUI
hideObj                 hideObj
histogramControlsUI     histogramControlsUI
installpack             installpack
kmeansControlsUI        kmeansControlsUI
lcfMetRadio             lcfMetRadio
loadpack                loadpack
mainPlotControlsUI      mainPlotControlsUI
mainScatterNew          mainScatterNew
niceKmeans              niceKmeans
normalizationMethods    normalizationMethods
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
prepDEOutput            prepDEOutput
prepDataContainer       prepDataContainer
prepGroup               prepGroup
prepHeatData            prepHeatData
prepPCADat              prepPCADat
push                    push
removeCols              removeCols
removeExtraCols         removeExtraCols
round_vals              round_vals
runDE                   runDE
runDESeq2               runDESeq2
runEdgeR                runEdgeR
runHeatmap              runHeatmap
runHeatmap2             runHeatmap2
runLimma                runLimma
run_pca                 run_pca
selectConditions        selectConditions
selectGroupInfo         selectGroupInfo
selectedInput           selectedInput
sepRadio                sepRadio
setBatch                setBatch to skip batch effect correction batch
                        variable set with the filter results
showObj                 showObj
startDEBrowser          startDEBrowser
startHeatmap            startHeatmap
textareaInput           textareaInput
togglePanels            togglePanels
