flowBin: Combining multitube flow cytometry data by binning
Version 1.12.0

Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.

AuthorKieran O'Neill
Bioconductor views CellBasedAssays FlowCytometry
Date of publicationNone
MaintainerKieran O'Neill <koneill@bccrc.ca>
LicenseArtistic-2.0
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowBin")

Popular man pages

BinnedFlowSample: A 'FlowSample', but with binning information for each tube
eventsInBins: Count number of events for each tube in each bin
flowFPBin: Bin sample using flowFP binning
FlowSample: A class similar to flowSet, but with extra information needed...
kMeansBin: Bin sample using K-means binning
mapBinsKNN: Internal function to map bins by KNN
show-methods: Methods to view flowBin objects
See all...

All man pages Function index File listing

Man pages

amlsample: Multitube AML sample as example data for flowBin
BinnedFlowSample: A 'FlowSample', but with binning information for each tube
checkQNorm: Function to check the quantile normalisation of a FlowSample...
eventsInBins: Count number of events for each tube in each bin
flowBin: function to run the entire flowBin pipeline
flowFPBin: Bin sample using flowFP binning
FlowSample: A class similar to flowSet, but with extra information needed...
getBinExpr: Calculate the expression of each bin in a BinnedFlowSample in...
kMeansBin: Bin sample using K-means binning
mapBinsKNN: Internal function to map bins by KNN
quantileNormalise: quantileNormalise normalise binning paramaters across all...
removeSparseBins: Remove bins from a BinnedFlowSample with few events in them
show-methods: Methods to view flowBin objects

Functions

BinnedFlowSample Man page
BinnedFlowSample-class Man page
FlowSample Man page
FlowSample-class Man page
aml.sample Man page
amlsample Man page
bin.labels Man page
bin.labels,BinnedFlowSample-method Man page
bin.labels<- Man page
bin.labels<-,BinnedFlowSample,list-method Man page
bin.pars Man page
bin.pars,FlowSample-method Man page
bin.pars<- Man page
bin.pars<-,FlowSample,vector-method Man page
checkQNorm Man page
checkQNorm, Man page
checkQNorm,FlowSample,FlowSample-method Man page
checkQNorm.func Source code
control.tubes Man page
control.tubes,FlowSample-method Man page
control.tubes<- Man page
control.tubes<-,FlowSample,vector-method Man page
eventsInBins Man page
eventsInBins,BinnedFlowSample-method Man page
flowBin Man page Source code
flowFPBin Man page
flowFPBin,FlowSample-method Man page
flowFPBin.def Source code
flowbin-package Man page
getBinExpr Man page
getBinExpr,BinnedFlowSample-method Man page
getBinExpr.def Source code
kMeansBin Man page
kMeansBin,FlowSample-method Man page
kMeansBin.def Source code
mapBinsKNN Man page
mapBinsKNN,FlowSample-method Man page
mapBinsKNN.def Source code
measure.pars Man page
measure.pars,FlowSample-method Man page
measure.pars<- Man page
measure.pars<-,FlowSample,list-method Man page
medianFI Source code
medianFIDist Source code
name Man page
name,FlowSample-method Man page
name<- Man page
name<-,FlowSample,character-method Man page
proportionPositive Source code
qnorm.func Source code
quantileNormalise Man page
quantileNormalise,FlowSample-method Man page
removeSparseBins Man page
removeSparseBins,BinnedFlowSample-method Man page
removeSparseBins.def Source code
show,BinnedFlowExprSet-method Man page
show,CVResult-method Man page
show,FlowSample-method Man page
show-methods Man page
tube.set Man page
tube.set,FlowSample-method Man page
tube.set<- Man page
tube.set<-,FlowSample,list-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/BinnedFlowSample-accessors.R
R/FlowSample-accessors.R
R/checkQNorm.R
R/flowBin.R
R/flowFPBin.R
R/getBinExpr.R
R/kMeansBin.R
R/mapClustersKNN.R
R/quantileNormalise.R
R/removeSparseBins.R
build
build/vignette.rds
data
data/amlsample.rda
inst
inst/NEWS
inst/doc
inst/doc/flowBin.R
inst/doc/flowBin.Rnw
inst/doc/flowBin.pdf
inst/examples
inst/examples/flowBin.R
inst/examples/flowFPBin.R
inst/examples/getBinExpr.R
inst/examples/kMeansBin.R
inst/examples/mapBinsKNN.R
inst/examples/quantileNormalise.R
man
man/BinnedFlowSample.Rd
man/FlowSample.Rd
man/amlsample.Rd
man/checkQNorm.Rd
man/eventsInBins.Rd
man/flowBin.Rd
man/flowFPBin.Rd
man/getBinExpr.Rd
man/kMeansBin.Rd
man/mapBinsKNN.Rd
man/quantileNormalise.Rd
man/removeSparseBins.Rd
man/show-methods.Rd
vignettes
vignettes/flowBin-stage0.pdf
vignettes/flowBin-stage1.pdf
vignettes/flowBin.Rnw
flowBin documentation built on May 20, 2017, 11 p.m.

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