flowUtils: Utilities for flow cytometry
Version 1.40.0

Provides utilities for flow cytometry data.

Browse man pages Browse package API and functions Browse package files

AuthorJ. Spidlen., N. Gopalakrishnan, F. Hahne, B. Ellis, R. Gentleman, M. Dalphin, N. Le Meur, B. Purcell, W. Jiang
Bioconductor views CellBasedAssays DecisionTree FlowCytometry Infrastructure
Date of publicationNone
MaintainerJosef Spidlen <jspidlen@gmail.com>
LicenseArtistic-2.0
Version1.40.0
URL https://github.com/jspidlen/flowUtils
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowUtils")

Man pages

flowUtil-package: Utilities for flow cytometry data
read.gatingML: Function to parse a Gating-ML XML file into objects in the R...
testGatingMLCompliance: Function to perform all the Gating-ML compliance tests
write.gatingML: Function to write a Gating-ML XML file based on gating and...

Functions

addAsinhtGml1.5 Source code
addAsinhtGml2 Source code
addBooleanAndGateNode Source code
addBooleanNotGateNode Source code
addBooleanOrGateNode Source code
addCompensation Source code
addCompensationRef Source code
addDebugMessage Source code
addDimensionContents Source code
addDimensions Source code
addEllipsoidGateNode Source code
addGateWithParent Source code
addHTMLExtensionIfNeeded Source code
addHyperlogtGml2 Source code
addLintGml2 Source code
addLogicletGml2 Source code
addLogtGml2 Source code
addObjectToGatingML Source code
addPolygonGateNode Source code
addQuadGateNode Source code
addRatioGml1.5 Source code
addRatiotGml2 Source code
addRectGateMinMax Source code
addRectangleGateNode Source code
addReferencedObjectsToEnv Source code
collectTransform Source code
createOrUseGml2RatioTransformation Source code
createOrUseGml2Transformation Source code
createTransformIdentifier Source code
decisionHelper Source code
dispatchGatingML2Transform Source code
dispatchTransform Source code
doubleCheckExistanceOfFilter Source code
doubleCheckExistanceOfParameter Source code
fasinhTr Source code
filterIdtoXMLId Source code
flinTr Source code
flogTr Source code
flowUtils Man page
flowUtils-package Man page
fratioTr Source code
genid Source code
getBounds Source code
getDetectorList Source code
getElementValueAsNumeric Source code
getFluorochromeList Source code
getGatingML2RatioParameterList Source code
getObjectId Source code
getParameterList Source code
getSide Source code
getTransformationList Source code
getTransformationListForQuadrantGate Source code
getTransformationListGml2 Source code
hyperlogTr Source code
internal.read.gatingML Man page
isIdWrittenToXMLAlready Source code
isNCNameChar Source code
logicleTr Source code
makeCall Source code
objectNameToObject Source code
onLoad Source code
performGateTest Source code
read.gatingML Man page Source code
resolveTransformationReference Source code
shouldTransformationBeSkipped Source code
smartTreeParse Source code
testGatingML1.5Compliance Source code
testGatingML2.0Compliance Source code
testGatingMLCompliance Man page Source code
transCompensation Source code
transDg1polynomial Source code
transEH Source code
transExponential Source code
transHyperLog Source code
transHyperbolicSin Source code
transInvSplitScale Source code
transInverseHyperbolicSin Source code
transLogarithm Source code
transQuadratic Source code
transRatio Source code
transSplitScale Source code
transSquareroot Source code
write.gatingML Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/compensation.R
R/gate-methods.R
R/gatingML.R
R/helperFunctions.R
R/parameter-methods.R
R/transforms.R
R/workflow2FlowJo.R
R/writeGatingML.R
R/zzz.R
build
build/vignette.rds
examples
examples/example1.R
examples/example2.R
examples/example3.R
examples/example4.R
inst
inst/RUnitGml2Script_Files
inst/RUnitGml2Script_Files/runit.01.set1.R
inst/RUnitGml2Script_Files/runit.02.set2.R
inst/RUnitGml2Script_Files/runit.03.set3.R
inst/RUnitGml2Script_Files/runit.04.set4.R
inst/RUnitGml2Script_Files/runit.05.set5.R
inst/RUnitGml2Script_Files/runit.writeGatingML2.set1.R
inst/RUnitGml2Script_Files/runit.writeGatingML2.set2.R
inst/RUnitGml2Script_Files/runit.writeGatingML2.set3.R
inst/RUnitGml2Script_Files/runit.writeGatingML2.set4.R
inst/RUnitGml2Script_Files/runit.writeGatingML2.set5.R
inst/RUnitGml2Script_Files/runit.writeGatingML2.set6.R
inst/RUnitScript_Files
inst/RUnitScript_Files/runit.01Rectangular.R
inst/RUnitScript_Files/runit.02CtSRectangular.R
inst/RUnitScript_Files/runit.03LargeRectangular.R
inst/RUnitScript_Files/runit.04PolygonGates.R
inst/RUnitScript_Files/runit.05CtSPolygonGates.R
inst/RUnitScript_Files/runit.06LargePolygons.R
inst/RUnitScript_Files/runit.07ComplicatedPolygons.R
inst/RUnitScript_Files/runit.08Ellipses.R
inst/RUnitScript_Files/runit.09Ellipsoid.R
inst/RUnitScript_Files/runit.10PolytopeGates.R
inst/RUnitScript_Files/runit.11DecisionTrees.R
inst/RUnitScript_Files/runit.12CtSDecisionTreeGates.R
inst/RUnitScript_Files/runit.13LargeDecisionTrees.R
inst/RUnitScript_Files/runit.14BooleanGates.R
inst/RUnitScript_Files/runit.15CtSBooleanGates.R
inst/RUnitScript_Files/runit.16LargeBooleanGates.R
inst/RUnitScript_Files/runit.17ParentIdTest.R
inst/RUnitScript_Files/runit.18ParentIdTest2.R
inst/RUnitScript_Files/runit.19TrCombination.R
inst/RUnitScript_Files/runit.20TrRatio.R
inst/RUnitScript_Files/runit.21TrQuadratic.R
inst/RUnitScript_Files/runit.22TrSqrt.R
inst/RUnitScript_Files/runit.23TrLn.R
inst/RUnitScript_Files/runit.24TrExp.R
inst/RUnitScript_Files/runit.25TrASinH.R
inst/RUnitScript_Files/runit.26TrSinH.R
inst/RUnitScript_Files/runit.27TrHyperlog.R
inst/RUnitScript_Files/runit.28TrEH.R
inst/RUnitScript_Files/runit.29TrSplitScale.R
inst/RUnitScript_Files/runit.30TrInvSplitScale.R
inst/RUnitScript_Files/runit.31TrCompensation.R
inst/RUnitScript_Files/runit.32TrCompensation.R
inst/defaults.xml
inst/doc
inst/doc/HowTo-flowUtils.R
inst/doc/HowTo-flowUtils.Rnw
inst/doc/HowTo-flowUtils.pdf
inst/extdata
inst/extdata/GatingML2.0_Example1.xml
man
man/flowUtil-package.Rd
man/read.gatingML.Rd
man/testGatingMLCompliance.Rd
man/write.gatingML.Rd
vignettes
vignettes/166889.png
vignettes/HowTo-flowUtils.Rnw
vignettes/flowUtilsRefs.bib
flowUtils documentation built on May 20, 2017, 10:06 p.m.