# debrowser: Interactive Differential Expresion Analysis Browser

## Documentation for package ‘debrowser’ version 1.6.8

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

## Help Pages

A B C D G H I L M P R S T V W

## -- A --

actionButton | Buttons including Action Buttons and Event Buttons
addDataCols | addDataCols
addID | addID
add_title_pos | add_title_pos
all2all | all2all
applyFilters | applyFilters
applyFiltersToMergedComparison | applyFiltersToMergedComparison

## -- B --

bookmarkServer | bookmarkServer
bookmarkUI | bookmarkUI

## -- C --

clusterData | clusterData
compareClust | compareClust
copy2newDirectory | copy2newDirectory
correctBatchEffect | Correct Batch Effect

## -- D --

deServer | deServer
deUI | deUI
drawPCAExplained | drawPCAExplained

## -- G --

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

## -- H --

hideObj | hideObj

## -- I --

installpack | installpack

## -- L --

link_brush | link_brush
loadpack | loadpack
load_data | load_data.
logSliderJScode | logSliderJScode

## -- M --

mainScatter | mainScatter
MAPlot | MAPlot
MAZoom | MAZoom

## -- P --

panel.cor | panel.cor
panel.hist | panel.hist
plot_pca | plot_pca
prepAddQCPlots | prepAddQCPlots
prepDataContainer | prepDataContainer
prepDataForQC | prepDataForQC
prepDEOutput | prepDEOutput
push | push

## -- R --

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

## -- S --

saveQCPlot | saveQCPlot
scatterZoom | scatterZoom
selectBatchEffect | selectBatchEffect
selectConditions | selectConditions
selectedInput | selectedInput
setFilterParams | setFilterParams
showObj | showObj
startDEBrowser | startDEBrowser

## -- T --

textareaInput | textareaInput
togglePanels | togglePanels

## -- V --

volcanoPlot | volcanoPlot
volcanoZoom | volcanoZoom

## -- W --

whitelist | Whitelist check