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| actionButton | Buttons including Action Buttons and Event Buttons |
| addDataCols | addDataCols |
| addID | addID |
| add_title_pos | add_title_pos |
| all2all | all2all |
| applyFilters | applyFilters |
| applyFiltersToMergedComparison | applyFiltersToMergedComparison |
| bookmarkServer | bookmarkServer |
| bookmarkUI | bookmarkUI |
| clusterData | clusterData |
| compareClust | compareClust |
| copy2newDirectory | copy2newDirectory |
| correctBatchEffect | Correct Batch Effect |
| deServer | deServer |
| deUI | deUI |
| drawPCAExplained | drawPCAExplained |
| getAfterLoadMsg | getAfterLoadMsg |
| getColors | getColors |
| getColorShapeSelection | getColorShapeSelection |
| getCompSelection | getCompSelection |
| getConditionSelector | getConditionSelector |
| getConditionSelectorFromMeta | getConditionSelectorFromMeta |
| getCondMsg | getCondMsg |
| getCutOffSelection | getCutOffSelection |
| getDataForTables | getDataForTables get data to fill up tables tab |
| getDataPrepPanel | getDataPrepPanel |
| getDensityPlot | getDensityPlot |
| getDomains | getDomains |
| getDown | getDown get down regulated data |
| getDownloadSection | getDownloadSection |
| getEnrichDO | getEnrichDO |
| getEnrichGO | getEnrichGO |
| getEnrichKEGG | getEnrichKEGG |
| getEntrezIds | getGeneList |
| getGeneList | getGeneList |
| getGeneSetData | getGeneSetData |
| getGOLeftMenu | getGOLeftMenu |
| getGoPanel | getGoPanel |
| getGOPlots | getGOPlots |
| getHelpButton | getHelpButton prepares a helpbutton for to go to a specific site in the documentation |
| getHoverPlots | getHoverPlots |
| getInitialMenu | getInitialMenu |
| getIntHeatmap | getIntHeatmap |
| getIntHeatmapVis | getIntHeatmapVis |
| getIQRPlot | getIQRPlot |
| getJsonObj | getJsonObj |
| getKEGGModal | getKEGGModal prepares a helpbutton for to go to a specific site in the documentation |
| getLeftMenu | getLeftMenu |
| getLegendSelect | getLegendSelect |
| getLoadingMsg | getLoadingMsg |
| getLogo | getLogo |
| getMainPanel | getMainPanel |
| getMainPanelPlots | getMainPanelPlots |
| getMainPlotsLeftMenu | getMainPlotsLeftMenu |
| getMean | getMean |
| getMergedComparison | getMergedComparison |
| getMethodDetails | get the detail boxes after DE method selected |
| getMostVariedList | getMostVariedList |
| getNormalizedMatrix | getNormalizedMatrix |
| getOrganism | getOrganism |
| getOrganismBox | getOrganismBox |
| getOrganismPathway | getOrganismPathway |
| getPCAexplained | getPCAexplained |
| getPCselection | getPCselection |
| getProgramTitle | getProgramTitle |
| getQCLeftMenu | getQCLeftMenu |
| getQCPanel | getQCPanel |
| getQCPlots | getQCPlots |
| getQCReplot | getQCReplot |
| getSampleNames | getSampleNames |
| getSamples | getSamples |
| getSearchData | getSearchData |
| getSelectedCols | getSelectedCols |
| getSelectedDatasetInput | getSelectedDatasetInput |
| getSelectInputBox | getSelectInputBox |
| getSelHeat | getSelHeat |
| getShapeColor | getShapeColor |
| getStartPlotsMsg | getStartPlotsMsg |
| getStartupMsg | getStartupMsg |
| getTableStyle | getTableStyle |
| getTextOnOff | getTextOnOff |
| getToolTipPCA | getToolTipPCA |
| getToolTipText | getToolTipText |
| getUp | getUp get up regulated data |
| getUpDown | getUpDown get up+down regulated data |
| get_state_id | get_state_id |
| get_user_info | Get the logged in user's email and other info |
| hideObj | hideObj |
| installpack | installpack |
| link_brush | link_brush |
| loadpack | loadpack |
| load_data | load_data. |
| logSliderJScode | logSliderJScode |
| mainScatter | mainScatter |
| MAPlot | MAPlot |
| MAZoom | MAZoom |
| panel.cor | panel.cor |
| panel.hist | panel.hist |
| plot_pca | plot_pca |
| prepAddQCPlots | prepAddQCPlots |
| prepDataContainer | prepDataContainer |
| prepDataForQC | prepDataForQC |
| prepDEOutput | prepDEOutput |
| push | push |
| readMetaData | readMetaData |
| removeBookmark | removeBookmark |
| removeCols | removeCols |
| round_vals | round_vals |
| runBayseq | runBayseq |
| runDE | runDE |
| runDESeq | runDESeq |
| runDESeq2 | runDESeq2 |
| runEdgeR | runEdgeR |
| runHeatmap | runHeatmap |
| runLimma | runLimma |
| run_pca | run_pca |
| saveQCPlot | saveQCPlot |
| scatterZoom | scatterZoom |
| selectBatchEffect | selectBatchEffect |
| selectConditions | selectConditions |
| selectedInput | selectedInput |
| setFilterParams | setFilterParams |
| showObj | showObj |
| startDEBrowser | startDEBrowser |
| textareaInput | textareaInput |
| togglePanels | togglePanels |
| volcanoPlot | volcanoPlot |
| volcanoZoom | volcanoZoom |
| whitelist | Whitelist check |