flowBin: Combining multitube flow cytometry data by binning

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.

Author
Kieran O'Neill
Date of publication
None
Maintainer
Kieran O'Neill <koneill@bccrc.ca>
License
Artistic-2.0
Version
1.10.0

View on Bioconductor

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

Files in this package

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