flowQ: Quality control for flow cytometry
Version 1.36.0

Provides quality control and quality assessment tools for flow cytometry data.

AuthorR. Gentleman, F. Hahne, J. Kettman, N. Le Meur, N. Gopalakrishnan
Bioconductor views CellBasedAssays FlowCytometry Infrastructure
Date of publicationNone
MaintainerMike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.36.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowQ")

Getting started

Package overview

Popular man pages

discreteAggregator-class: Class "discreteAggregator"
factorAggregator-class: Class "factorAggregator"
flowQ-package: Quality control for flow cytometry
numericAggregator-class: Class "numericAggregator"
qaGraph-class: Class "qaGraph"
qaProcess.BoundaryPlot: Creates a QA process for comparison of the percentage of...
qaProcess.ECDFPlot: Creates a QA process for comparisons of ECDF's across...
See all...

All man pages Function index File listing

Man pages

aggregatorList-class: Class "aggregatorList"
binaryAggregator-class: Class "binaryAggregator"
discreteAggregator-class: Class "discreteAggregator"
evaluateProcess: Evaluate QA processes
factorAggregator-class: Class "factorAggregator"
flowQ-package: Quality control for flow cytometry
locateDuplicatedParameters: Locate Duplicated Parameters
normalizeSets: Locate Duplicated Parameters
numericAggregator-class: Class "numericAggregator"
outlier-class: Virtual Class "outlier"
outlierResult-class: Class "outlierResult"
outliers-methods: ~~ Methods for Function outliers in Package '.GlobalEnv' ~~
preProcessFlowList: Preprocess a list of flowSets to add empty flowFrames for...
qaAggregator-class: Abstraction of the possible outcomes of a QA process
qaGraph-class: Class "qaGraph"
qaGraphList-class: Class "qaGraphList"
qaProcess.2DStatsPlot: Creates a QA process for 2D summary statistic comparisons...
qaProcess.BoundaryPlot: Creates a QA process for comparison of the percentage of...
qaProcess.cellnumber: Create QA process of type 'cellnumber'
qaProcess-class: Abstraction of the results of a QA process
qaProcess.DensityPlot: Creates a QA process for comparisons of density plots across...
qaProcess.ECDFPlot: Creates a QA process for comparisons of ECDF's across...
qaProcessFrame-class: Class "qaProcessFrame"
qaProcess.KLDistPlot: Creates a QA process for comparisons of KL Distances across...
qaProcess.marginevents: Create QA process of type 'marginevents'
qaProcessSummary-class: Class "qaProcessSummary"
qaProcess.timeflow: Create QA process of type 'timeflow'
qaProcess.timeline: Create QA process of type 'timeline'
qaReport: Create HTML report using one or several QA process...
qData: Data for demonstrating QA processes that compares dye...
rangeAggregator-class: Class "rangeAggregator"
stringAggregator-class: Class "stringAggregator"
txtFormatQAObject: Formats results contained in QA process objects into a data...
validProcess: Validate a QAProcess object
writeQAReport: Create HTML report for (lists of) qaProcess objects
writeQATextReport: Create tab delimited text files for (lists of) qaProcess...

Functions

aggregatorList Man page Source code
aggregatorList-class Man page
binaryAggregator Man page Source code
binaryAggregator-class Man page
checkClass Source code
checkInputs Source code
cnams Source code
combineAltCols Source code
constructPath Source code
copyGraphs Source code
createImageDir Source code
discreteAggregator Man page Source code
discreteAggregator-class Man page
evaluateProcess Man page Source code
factorAggregator Man page Source code
factorAggregator-class Man page
failedProcesses Source code
flowQ Man page
flowQ-package Man page
guid Source code
htmlBarplot Source code
initialize,aggregatorList-method Man page
initialize,qaGraph-method Man page
initialize,qaGraphList-method Man page
initialize,qaProcess-method Man page
initialize,qaProcessFrame-method Man page
locateDuplicatedParameters Man page Source code
locateParameter Source code
myOpenHtmlPage Source code
mySd Source code
mybw.nrd0 Source code
names,qaGraph-method Man page
normalizeSets Man page Source code
numericAggregator Man page Source code
numericAggregator-class Man page
onAttach Source code
outlier-class Man page
outlierD Source code
outlierG Source code
outlierResult-class Man page
outlierX2 Source code
outliers Man page
outliers,flowSet-method Man page
outliers-methods Man page
pdfLink Source code
preProcessFlowList Man page Source code
qData Man page
qaAggregator Man page
qaAggregator-class Man page
qaGraph Man page Source code
qaGraph-class Man page
qaGraphList Man page Source code
qaGraphList-class Man page
qaProcess Man page Source code
qaProcess-class Man page
qaProcess.2DStatsPlot Man page Source code
qaProcess.BoundaryPlot Man page Source code
qaProcess.DensityPlot Man page Source code
qaProcess.ECDFPlot Man page Source code
qaProcess.KLDistPlot Man page Source code
qaProcess.cellnumber Man page Source code
qaProcess.marginevents Man page Source code
qaProcess.timeflow Man page Source code
qaProcess.timeline Man page Source code
qaProcessFrame Man page Source code
qaProcessFrame-class Man page
qaProcessSummary Man page
qaProcessSummary-class Man page
qaReport Man page Source code
rangeAggregator Man page Source code
rangeAggregator-class Man page
shortNames Source code
show,aggregatorList-method Man page
show,binaryAggregator-method Man page
show,discreteAggregator-method Man page
show,factorAggregator-method Man page
show,numericAggregator-method Man page
show,qaGraph-method Man page
show,qaGraphList-method Man page
show,qaProcess-method Man page
show,qaProcessFrame-method Man page
show,qaProcessSummary-method Man page
show,rangeAggregator-method Man page
show,stringAggregator-method Man page
stringAggregator Man page Source code
stringAggregator-class Man page
txtFormatQAObject Man page Source code
validProcess Man page Source code
win2UnixPath Source code
writeLines,binaryAggregator,file,missing,missing-method Man page
writeLines,data.frame,file,missing,missing-method Man page
writeLines,discreteAggregator,file,missing,missing-method Man page
writeLines,factorAggregator,file,missing,missing-method Man page
writeLines,numericAggregator,file,missing,missing-method Man page
writeLines,qaProcessSummary,file,missing,missing-method Man page
writeLines,rangeAggregator,file,missing,missing-method Man page
writeLines,stringAggregator,file,missing,missing-method Man page
writeQAReport Man page Source code
writeQATextReport Man page Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/aggregator-accessors.R
R/evaluateProcess.R
R/flowSet-methods.R
R/misc-methods.R
R/qaGraph-accessors.R
R/qaProcess-accessors.R
R/qaProcessFunctions.R
R/qaReport.R
R/zzz.R
build
build/vignette.rds
data
data/datalist
data/qData.rda
inst
inst/doc
inst/doc/DataQualityAssessment.R
inst/doc/DataQualityAssessment.Rnw
inst/doc/DataQualityAssessment.pdf
inst/doc/Extending-flowQ.R
inst/doc/Extending-flowQ.Rnw
inst/doc/Extending-flowQ.pdf
inst/htmlTemplates
inst/htmlTemplates/bulbGreen.png
inst/htmlTemplates/bulbRed.png
inst/htmlTemplates/bulbYellow.png
inst/htmlTemplates/qaReport.css
inst/htmlTemplates/qaReport.js
inst/htmlTemplates/scalelefteven.gif
inst/htmlTemplates/scaleleftodd.gif
inst/htmlTemplates/scalemiddleeven.gif
inst/htmlTemplates/scalemiddleodd.gif
inst/htmlTemplates/scalerighteven.gif
inst/htmlTemplates/scalerightodd.gif
inst/htmlTemplates/scalesingleeven.gif
inst/htmlTemplates/scalesingleodd.gif
man
man/aggregatorList-class.Rd
man/binaryAggregator-class.Rd
man/discreteAggregator-class.Rd
man/evaluateProcess.Rd
man/factorAggregator-class.Rd
man/flowQ-package.Rd
man/locateDuplicatedParameters.Rd
man/normalizeSets.Rd
man/numericAggregator-class.Rd
man/outlier-class.Rd
man/outlierResult-class.Rd
man/outliers-methods.Rd
man/preProcessFlowList.Rd
man/qData.Rd
man/qaAggregator-class.Rd
man/qaGraph-class.Rd
man/qaGraphList-class.Rd
man/qaProcess-class.Rd
man/qaProcess.2DStatsPlot.Rd
man/qaProcess.BoundaryPlot.Rd
man/qaProcess.DensityPlot.Rd
man/qaProcess.ECDFPlot.Rd
man/qaProcess.KLDistPlot.Rd
man/qaProcess.cellnumber.Rd
man/qaProcess.marginevents.Rd
man/qaProcess.timeflow.Rd
man/qaProcess.timeline.Rd
man/qaProcessFrame-class.Rd
man/qaProcessSummary-class.Rd
man/qaReport.Rd
man/rangeAggregator-class.Rd
man/stringAggregator-class.Rd
man/txtFormatQAObject.Rd
man/validProcess.Rd
man/writeQAReport.Rd
man/writeQATextReport.Rd
vignettes
vignettes/DataQualityAssessment.Rnw
vignettes/Extending-flowQ.Rnw
vignettes/binary.jpg
vignettes/cytoref.bib
vignettes/discrete.jpg
vignettes/factor.jpg
vignettes/flowQStructure.pdf
vignettes/images
vignettes/images/bulbGreen.png
vignettes/images/bulbRed.png
vignettes/images/bulbYellow.png
vignettes/images/qaReport.css
vignettes/images/qaReport.js
vignettes/numeric.jpg
vignettes/range.jpg
vignettes/stainInfo.pdf
vignettes/string.jpg
flowQ documentation built on May 20, 2017, 9:22 p.m.

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