debrowser: debrowser: Interactive Differential Expresion Analysis Browser

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Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, user can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With this system users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.

Author
Alper Kucukural <alper.kucukural@umassmed.edu>, Nicholas Merowsky <nicholas.merowsky@umassmed.edu>, Manuel Garber <manuel.garber@umassmed.edu>
Date of publication
None
Maintainer
Alper Kucukural <alper.kucukural@umassmed.edu>
License
GPL-3 + file LICENSE
Version
1.2.3
URLs

View on Bioconductor

Man pages

actionButton
Buttons including Action Buttons and Event Buttons
addID
addID
add_title_pos
add_title_pos
all2all
all2all
applyFilters
applyFilters
applyFiltersToMergedComparison
applyFiltersToMergedComparison
clusterData
clusterData
compareClust
compareClust
correctBatchEffect
Correct Batch Effect
deServer
deServer
deUI
deUI
drawPCAExplained
drawPCAExplained
getAfterLoadMsg
getAfterLoadMsg
getColors
getColors
getColorShapeSelection
getColorShapeSelection
getCompSelection
getCompSelection
getConditionSelector
getConditionSelector
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
getGeneList
getGeneList
getGeneSetData
getGeneSetData
getGOLeftMenu
getGOLeftMenu
getGoPanel
getGoPanel
getGOPlots
getGOPlots
getHelpButton
getHelpButton prepares a helpbutton for to go to a specific...
getHoverPlots
getHoverPlots
getInitialMenu
getInitialMenu
getIntHeatmap
getIntHeatmap
getIntHeatmapVis
getIntHeatmapVis
getIQRPlot
getIQRPlot
getLeftMenu
getLeftMenu
getLegendSelect
getLegendSelect
getLoadingMsg
getLoadingMsg
getLogo
getLogo
getMainPanel
getMainPanel
getMainPanelPlots
getMainPanelPlots
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
hideObj
hideObj
installpack
installpack
link_brush
link_brush
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
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

Files in this package

debrowser/DESCRIPTION
debrowser/LICENSE
debrowser/NAMESPACE
debrowser/NEWS
debrowser/R
debrowser/R/GOterm.R
debrowser/R/MAPlot.R
debrowser/R/QCSection.R
debrowser/R/all2all.R
debrowser/R/condSelect.R
debrowser/R/deprogs.R
debrowser/R/deseq2.R
debrowser/R/downloadSection.R
debrowser/R/funcs.R
debrowser/R/gopanel.R
debrowser/R/heatmap.R
debrowser/R/installpack.R
debrowser/R/link_brush.R
debrowser/R/load_data.R
debrowser/R/mainScatter.R
debrowser/R/mainpanel.R
debrowser/R/normalization.R
debrowser/R/pca.R
debrowser/R/plot_props.R
debrowser/R/prepdata.R
debrowser/R/sampleNames.R
debrowser/R/server.R
debrowser/R/startShiny.R
debrowser/R/ui.R
debrowser/R/uifuncs.R
debrowser/R/volcano.R
debrowser/README.md
debrowser/README.pdf
debrowser/build
debrowser/build/vignette.rds
debrowser/debrowser.Rproj
debrowser/inst
debrowser/inst/doc
debrowser/inst/doc/DEBrowser.R
debrowser/inst/doc/DEBrowser.Rmd
debrowser/inst/doc/DEBrowser.html
debrowser/inst/extdata
debrowser/inst/extdata/demo
debrowser/inst/extdata/demo/demodata.Rda
debrowser/inst/extdata/www
debrowser/inst/extdata/www/favicon.ico
debrowser/inst/extdata/www/images
debrowser/inst/extdata/www/images/initial_loading.gif
debrowser/inst/extdata/www/images/loading.gif
debrowser/inst/extdata/www/images/logo.png
debrowser/man
debrowser/man/MAPlot.Rd
debrowser/man/MAZoom.Rd
debrowser/man/actionButton.Rd
debrowser/man/addID.Rd
debrowser/man/add_title_pos.Rd
debrowser/man/all2all.Rd
debrowser/man/applyFilters.Rd
debrowser/man/applyFiltersToMergedComparison.Rd
debrowser/man/clusterData.Rd
debrowser/man/compareClust.Rd
debrowser/man/correctBatchEffect.Rd
debrowser/man/deServer.Rd
debrowser/man/deUI.Rd
debrowser/man/drawPCAExplained.Rd
debrowser/man/getAfterLoadMsg.Rd
debrowser/man/getColorShapeSelection.Rd
debrowser/man/getColors.Rd
debrowser/man/getCompSelection.Rd
debrowser/man/getCondMsg.Rd
debrowser/man/getConditionSelector.Rd
debrowser/man/getCutOffSelection.Rd
debrowser/man/getDataForTables.Rd
debrowser/man/getDataPrepPanel.Rd
debrowser/man/getDensityPlot.Rd
debrowser/man/getDomains.Rd
debrowser/man/getDown.Rd
debrowser/man/getDownloadSection.Rd
debrowser/man/getEnrichDO.Rd
debrowser/man/getEnrichGO.Rd
debrowser/man/getEnrichKEGG.Rd
debrowser/man/getGOLeftMenu.Rd
debrowser/man/getGOPlots.Rd
debrowser/man/getGeneList.Rd
debrowser/man/getGeneSetData.Rd
debrowser/man/getGoPanel.Rd
debrowser/man/getHelpButton.Rd
debrowser/man/getHoverPlots.Rd
debrowser/man/getIQRPlot.Rd
debrowser/man/getInitialMenu.Rd
debrowser/man/getIntHeatmap.Rd
debrowser/man/getIntHeatmapVis.Rd
debrowser/man/getLeftMenu.Rd
debrowser/man/getLegendSelect.Rd
debrowser/man/getLoadingMsg.Rd
debrowser/man/getLogo.Rd
debrowser/man/getMainPanel.Rd
debrowser/man/getMainPanelPlots.Rd
debrowser/man/getMean.Rd
debrowser/man/getMergedComparison.Rd
debrowser/man/getMethodDetails.Rd
debrowser/man/getMostVariedList.Rd
debrowser/man/getNormalizedMatrix.Rd
debrowser/man/getOrganism.Rd
debrowser/man/getOrganismBox.Rd
debrowser/man/getOrganismPathway.Rd
debrowser/man/getPCAexplained.Rd
debrowser/man/getPCselection.Rd
debrowser/man/getProgramTitle.Rd
debrowser/man/getQCLeftMenu.Rd
debrowser/man/getQCPanel.Rd
debrowser/man/getQCPlots.Rd
debrowser/man/getQCReplot.Rd
debrowser/man/getSampleNames.Rd
debrowser/man/getSamples.Rd
debrowser/man/getSearchData.Rd
debrowser/man/getSelHeat.Rd
debrowser/man/getSelectInputBox.Rd
debrowser/man/getSelectedCols.Rd
debrowser/man/getSelectedDatasetInput.Rd
debrowser/man/getShapeColor.Rd
debrowser/man/getStartPlotsMsg.Rd
debrowser/man/getStartupMsg.Rd
debrowser/man/getTableStyle.Rd
debrowser/man/getTextOnOff.Rd
debrowser/man/getToolTipPCA.Rd
debrowser/man/getToolTipText.Rd
debrowser/man/getUp.Rd
debrowser/man/getUpDown.Rd
debrowser/man/hideObj.Rd
debrowser/man/installpack.Rd
debrowser/man/link_brush.Rd
debrowser/man/load_data.Rd
debrowser/man/logSliderJScode.Rd
debrowser/man/mainScatter.Rd
debrowser/man/panel.cor.Rd
debrowser/man/panel.hist.Rd
debrowser/man/plot_pca.Rd
debrowser/man/prepAddQCPlots.Rd
debrowser/man/prepDEOutput.Rd
debrowser/man/prepDataContainer.Rd
debrowser/man/prepDataForQC.Rd
debrowser/man/push.Rd
debrowser/man/readMetaData.Rd
debrowser/man/removeCols.Rd
debrowser/man/round_vals.Rd
debrowser/man/runBayseq.Rd
debrowser/man/runDE.Rd
debrowser/man/runDESeq.Rd
debrowser/man/runDESeq2.Rd
debrowser/man/runEdgeR.Rd
debrowser/man/runHeatmap.Rd
debrowser/man/runLimma.Rd
debrowser/man/run_pca.Rd
debrowser/man/saveQCPlot.Rd
debrowser/man/scatterZoom.Rd
debrowser/man/selectBatchEffect.Rd
debrowser/man/selectConditions.Rd
debrowser/man/selectedInput.Rd
debrowser/man/setFilterParams.Rd
debrowser/man/showObj.Rd
debrowser/man/startDEBrowser.Rd
debrowser/man/textareaInput.Rd
debrowser/man/togglePanels.Rd
debrowser/man/volcanoPlot.Rd
debrowser/man/volcanoZoom.Rd
debrowser/svn-commit.tmp
debrowser/tests
debrowser/tests/test-demo.R
debrowser/tests/test-deseq.R
debrowser/tests/test-null.R
debrowser/tests/test-ui.R
debrowser/vignettes
debrowser/vignettes/DEBrowser.Rmd