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, 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.

AuthorAlper Kucukural <alper.kucukural@umassmed.edu>, Nicholas Merowsky <nicholas.merowsky@umassmed.edu>, Manuel Garber <manuel.garber@umassmed.edu>
Date of publicationNone
MaintainerAlper Kucukural <alper.kucukural@umassmed.edu>
LicenseGPL-3 + file LICENSE
Version1.2.4
https://github.com/UMMS-Biocore/debrowser

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

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