debrowser: debrowser: Interactive Differential Expresion Analysis Browser

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, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser 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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("debrowser")
AuthorAlper Kucukural <alper.kucukural@umassmed.edu>, Manuel Garber <manuel.garber@umassmed.edu>
Bioconductor views ChIPSeq Clustering DifferentialExpression GeneExpression RNASeq Sequencing
Date of publicationNone
MaintainerAlper Kucukural <alper.kucukural@umassmed.edu>
LicenseGPL-3 + file LICENSE
Version1.3.11
https://github.com/UMMS-Biocore/debrowser

View on Bioconductor

Man pages

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

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

getJsonObj: getJsonObj

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

get_state_id: get_state_id

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.

loadpack: loadpack

loadpacks: loadpacks

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

Functions

actionButton Man page
addDataCols Man page
addID Man page
add_title_pos Man page
all2all Man page
applyFilters Man page
applyFiltersToMergedComparison Man page
bookmarkServer Man page
bookmarkUI Man page
clusterData Man page
compareClust Man page
copy2newDirectory Man page
correctBatchEffect Man page
deServer Man page
deUI Man page
drawPCAExplained Man page
getAfterLoadMsg Man page
getColors Man page
getColorShapeSelection Man page
getCompSelection Man page
getConditionSelector Man page
getConditionSelectorFromMeta Man page
getCondMsg Man page
getCutOffSelection Man page
getDataForTables Man page
getDataPrepPanel Man page
getDensityPlot Man page
getDomains Man page
getDown Man page
getDownloadSection Man page
getEnrichDO Man page
getEnrichGO Man page
getEnrichKEGG Man page
getGeneList Man page
getGeneSetData Man page
getGOLeftMenu Man page
getGoPanel Man page
getGOPlots Man page
getHelpButton Man page
getHoverPlots Man page
getInitialMenu Man page
getIntHeatmap Man page
getIntHeatmapVis Man page
getIQRPlot Man page
getJsonObj Man page
getLeftMenu Man page
getLegendSelect Man page
getLoadingMsg Man page
getLogo Man page
getMainPanel Man page
getMainPanelPlots Man page
getMainPlotsLeftMenu Man page
getMean Man page
getMergedComparison Man page
getMethodDetails Man page
getMostVariedList Man page
getNormalizedMatrix Man page
getOrganism Man page
getOrganismBox Man page
getOrganismPathway Man page
getPCAexplained Man page
getPCselection Man page
getProgramTitle Man page
getQCLeftMenu Man page
getQCPanel Man page
getQCPlots Man page
getQCReplot Man page
getSampleNames Man page
getSamples Man page
getSearchData Man page
getSelectedCols Man page
getSelectedDatasetInput Man page
getSelectInputBox Man page
getSelHeat Man page
getShapeColor Man page
getStartPlotsMsg Man page
getStartupMsg Man page
get_state_id Man page
getTableStyle Man page
getTextOnOff Man page
getToolTipPCA Man page
getToolTipText Man page
getUp Man page
getUpDown Man page
hideObj Man page
installpack Man page
link_brush Man page
load_data Man page
loadpack Man page
loadpacks Man page
logSliderJScode Man page
mainScatter Man page
MAPlot Man page
MAZoom Man page
panel.cor Man page
panel.hist Man page
plot_pca Man page
prepAddQCPlots Man page
prepDataContainer Man page
prepDataForQC Man page
prepDEOutput Man page
push Man page
readMetaData Man page
removeBookmark Man page
removeCols Man page
round_vals Man page
runBayseq Man page
runDE Man page
runDESeq Man page
runDESeq2 Man page
runEdgeR Man page
runHeatmap Man page
runLimma Man page
run_pca Man page
saveQCPlot Man page
scatterZoom Man page
selectBatchEffect Man page
selectConditions Man page
selectedInput Man page
setFilterParams Man page
showObj Man page
startDEBrowser Man page
textareaInput Man page
togglePanels Man page
volcanoPlot Man page
volcanoZoom Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/GOterm.R R/MAPlot.R R/QCSection.R R/all2all.R R/bookmark.R R/condSelect.R R/deprogs.R R/deseq2.R R/downloadSection.R R/funcs.R R/gopanel.R R/heatmap.R R/installpack.R R/link_brush.R R/load_data.R R/mainScatter.R R/mainpanel.R R/normalization.R R/pca.R R/plot_props.R R/prepdata.R R/sampleNames.R R/server.R R/startShiny.R R/ui.R R/uifuncs.R R/volcano.R
README.md
README.pdf
build
build/vignette.rds
debrowser.Rproj
inst
inst/doc
inst/doc/DEBrowser.R
inst/doc/DEBrowser.Rmd
inst/doc/DEBrowser.html
inst/extdata
inst/extdata/demo
inst/extdata/demo/demodata.Rda
inst/extdata/www
inst/extdata/www/favicon.ico
inst/extdata/www/images
inst/extdata/www/images/delete_button.png
inst/extdata/www/images/initial_loading.gif
inst/extdata/www/images/loading.gif
inst/extdata/www/images/loading2.gif
inst/extdata/www/images/loading_start.gif
inst/extdata/www/images/logo.png
inst/extdata/www/shinydashboard_additional.css
man
man/MAPlot.Rd man/MAZoom.Rd man/actionButton.Rd man/addDataCols.Rd man/addID.Rd man/add_title_pos.Rd man/all2all.Rd man/applyFilters.Rd man/applyFiltersToMergedComparison.Rd man/bookmarkServer.Rd man/bookmarkUI.Rd man/clusterData.Rd man/compareClust.Rd man/copy2newDirectory.Rd man/correctBatchEffect.Rd man/deServer.Rd man/deUI.Rd man/drawPCAExplained.Rd man/getAfterLoadMsg.Rd man/getColorShapeSelection.Rd man/getColors.Rd man/getCompSelection.Rd man/getCondMsg.Rd man/getConditionSelector.Rd man/getConditionSelectorFromMeta.Rd man/getCutOffSelection.Rd man/getDataForTables.Rd man/getDataPrepPanel.Rd man/getDensityPlot.Rd man/getDomains.Rd man/getDown.Rd man/getDownloadSection.Rd man/getEnrichDO.Rd man/getEnrichGO.Rd man/getEnrichKEGG.Rd man/getGOLeftMenu.Rd man/getGOPlots.Rd man/getGeneList.Rd man/getGeneSetData.Rd man/getGoPanel.Rd man/getHelpButton.Rd man/getHoverPlots.Rd man/getIQRPlot.Rd man/getInitialMenu.Rd man/getIntHeatmap.Rd man/getIntHeatmapVis.Rd man/getJsonObj.Rd man/getLeftMenu.Rd man/getLegendSelect.Rd man/getLoadingMsg.Rd man/getLogo.Rd man/getMainPanel.Rd man/getMainPanelPlots.Rd man/getMainPlotsLeftMenu.Rd man/getMean.Rd man/getMergedComparison.Rd man/getMethodDetails.Rd man/getMostVariedList.Rd man/getNormalizedMatrix.Rd man/getOrganism.Rd man/getOrganismBox.Rd man/getOrganismPathway.Rd man/getPCAexplained.Rd man/getPCselection.Rd man/getProgramTitle.Rd man/getQCLeftMenu.Rd man/getQCPanel.Rd man/getQCPlots.Rd man/getQCReplot.Rd man/getSampleNames.Rd man/getSamples.Rd man/getSearchData.Rd man/getSelHeat.Rd man/getSelectInputBox.Rd man/getSelectedCols.Rd man/getSelectedDatasetInput.Rd man/getShapeColor.Rd man/getStartPlotsMsg.Rd man/getStartupMsg.Rd man/getTableStyle.Rd man/getTextOnOff.Rd man/getToolTipPCA.Rd man/getToolTipText.Rd man/getUp.Rd man/getUpDown.Rd man/get_state_id.Rd man/hideObj.Rd man/installpack.Rd man/link_brush.Rd man/load_data.Rd man/loadpack.Rd man/loadpacks.Rd man/logSliderJScode.Rd man/mainScatter.Rd man/panel.cor.Rd man/panel.hist.Rd man/plot_pca.Rd man/prepAddQCPlots.Rd man/prepDEOutput.Rd man/prepDataContainer.Rd man/prepDataForQC.Rd man/push.Rd man/readMetaData.Rd man/removeBookmark.Rd man/removeCols.Rd man/round_vals.Rd man/runBayseq.Rd man/runDE.Rd man/runDESeq.Rd man/runDESeq2.Rd man/runEdgeR.Rd man/runHeatmap.Rd man/runLimma.Rd man/run_pca.Rd man/saveQCPlot.Rd man/scatterZoom.Rd man/selectBatchEffect.Rd man/selectConditions.Rd man/selectedInput.Rd man/setFilterParams.Rd man/showObj.Rd man/startDEBrowser.Rd man/textareaInput.Rd man/togglePanels.Rd man/volcanoPlot.Rd man/volcanoZoom.Rd
svn-commit.tmp
tests
tests/test-demo.R tests/test-deseq.R tests/test-null.R tests/test-ui.R
vignettes
vignettes/DEBrowser.Rmd

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