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A B C D F G H I K L M N P R S T
| 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 |
| BoxMainPlotControlsUI | BoxMainPlotControlsUI |
| 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 |
| 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. |
| fileTypes | fileTypes |
| fileUploadBox | fileUploadBox |
| 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 |
| 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 |
| 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 |
| getSamples | getSamples |
| 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 |
| 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 |
| IQRPlotControlsUI | IQRPlotControlsUI |
| 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 |
| prepDataContainer | prepDataContainer |
| prepDEOutput | prepDEOutput |
| 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 |
| 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 |
| textareaInput | textareaInput |
| togglePanels | togglePanels |