flowQ: Quality control for flow cytometry

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

AuthorR. Gentleman, F. Hahne, J. Kettman, N. Le Meur, N. Gopalakrishnan
Date of publicationNone
MaintainerMike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.34.0

View on Bioconductor

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
aggregatorList-class Man page
binaryAggregator Man page
binaryAggregator-class Man page
discreteAggregator Man page
discreteAggregator-class Man page
evaluateProcess Man page
factorAggregator Man page
factorAggregator-class Man page
flowQ Man page
flowQ-package Man page
initialize,aggregatorList-method Man page
initialize,qaGraphList-method Man page
initialize,qaGraph-method Man page
initialize,qaProcessFrame-method Man page
initialize,qaProcess-method Man page
locateDuplicatedParameters Man page
names,qaGraph-method Man page
normalizeSets Man page
numericAggregator Man page
numericAggregator-class Man page
outlier-class Man page
outlierResult-class Man page
outliers Man page
outliers,flowSet-method Man page
outliers-methods Man page
preProcessFlowList Man page
qaAggregator Man page
qaAggregator-class Man page
qaGraph Man page
qaGraph-class Man page
qaGraphList Man page
qaGraphList-class Man page
qaProcess Man page
qaProcess.2DStatsPlot Man page
qaProcess.BoundaryPlot Man page
qaProcess.cellnumber Man page
qaProcess-class Man page
qaProcess.DensityPlot Man page
qaProcess.ECDFPlot Man page
qaProcessFrame Man page
qaProcessFrame-class Man page
qaProcess.KLDistPlot Man page
qaProcess.marginevents Man page
qaProcessSummary Man page
qaProcessSummary-class Man page
qaProcess.timeflow Man page
qaProcess.timeline Man page
qaReport Man page
qData Man page
rangeAggregator Man page
rangeAggregator-class Man page
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,qaGraphList-method Man page
show,qaGraph-method Man page
show,qaProcessFrame-method Man page
show,qaProcess-method Man page
show,qaProcessSummary-method Man page
show,rangeAggregator-method Man page
show,stringAggregator-method Man page
stringAggregator Man page
stringAggregator-class Man page
txtFormatQAObject Man page
validProcess Man page
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
writeQATextReport Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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