flowStats: Statistical methods for the analysis of flow cytometry data

Share:

Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.

Author
Florian Hahne, Nishant Gopalakrishnan, Alireza Hadj Khodabakhshi, Chao-Jen Wong, Kyongryun Lee
Date of publication
None
Maintainer
Greg Finak <gfinak@fhcrc.org> and Mike Jiang <wjiang2@fhcrc.org>
License
Artistic-2.0
Version
3.32.0

View on Bioconductor

Man pages

autoGate
Automated gating of single populations in 2D
BackGating
Sample backgating results
binByRef
Bin a test data set using bins previously created by...
calcPBChiSquare
Probability binning metirc for comparing the probability...
calcPearsonChi
Pearsons chi-square statistic for comparing the probability...
curv1Filter-class
Class "curv1Filter"
curv2Filter-class
Class "curv2Filter"
curvPeaks
Parse curv1Filter output
density1d
Find most likely separation between positive and negative...
flowStats-package
Statistical methods for flow cytometry data analysis
gaussNorm
Per-channel normalization based on landmark registration
gpaSet
Multi-dimensional normalization of flow cytometry data
idFeaturesByBackgating
(Internal use only) Identify features of flow cytometry data...
iProcrustes
Procrustes analysis. Using singular value decomposition (SVD)...
ITN
Sample flow cytometry data
landmarkMatrix
Compute and cluster high density regions in 1D
lymphGate
Automated gating of elliptical cell populations in 2D.
normalize
normalize a GatingSet imported with flowWorkspace, using...
normQA
Normalization quality assessment
plotBins
Plots the probability bins overlaid with flowFrame data
proBin
Probability binning - a metric for evaluating multivariate...
quadrantGate
Automated quad gating
rangeGate
Find most likely separation between positive and negative...
singletGate
Creates a singlet polygon gate using the prediction bands...
warpSet
Normalization based on landmark registration

Files in this package

flowStats/DESCRIPTION
flowStats/NAMESPACE
flowStats/NEWS
flowStats/R
flowStats/R/autoGate.R
flowStats/R/curvFilter-methods.R
flowStats/R/curvPeaks.R
flowStats/R/density1d.R
flowStats/R/dfltCounts.R
flowStats/R/drvkde.R
flowStats/R/fda_functions.R
flowStats/R/feature.R
flowStats/R/gaussNorm.R
flowStats/R/getPeakRegions.R
flowStats/R/gpaSet.R
flowStats/R/iProcrustes.R
flowStats/R/idFeatures.R
flowStats/R/landmarkMatrix.R
flowStats/R/landmarkMatrixWithoutFilterResult.R
flowStats/R/normalize-methods.R
flowStats/R/pbin.R
flowStats/R/pcout.R
flowStats/R/peakSeparator.R
flowStats/R/quadrantGate.R
flowStats/R/singletGate.R
flowStats/R/warpSet.R
flowStats/build
flowStats/build/vignette.rds
flowStats/data
flowStats/data/BackGating.rda
flowStats/data/ITN.rda
flowStats/data/datalist
flowStats/inst
flowStats/inst/doc
flowStats/inst/doc/GettingStartedWithFlowStats.R
flowStats/inst/doc/GettingStartedWithFlowStats.Rnw
flowStats/inst/doc/GettingStartedWithFlowStats.pdf
flowStats/man
flowStats/man/BackGating.Rd
flowStats/man/ITN.Rd
flowStats/man/autoGate.Rd
flowStats/man/binByRef.Rd
flowStats/man/calcPBChiSquare.Rd
flowStats/man/calcPearsonChi.Rd
flowStats/man/curv1Filter-class.Rd
flowStats/man/curv2Filter-class.Rd
flowStats/man/curvPeaks.Rd
flowStats/man/density1d.Rd
flowStats/man/flowStats-package.Rd
flowStats/man/gaussNorm.Rd
flowStats/man/gpaSet.Rd
flowStats/man/iProcrustes.Rd
flowStats/man/idFeaturesByBackgating.Rd
flowStats/man/landmarkMatrix.Rd
flowStats/man/lymphGate.Rd
flowStats/man/normQA.Rd
flowStats/man/normalize.Rd
flowStats/man/plotBins.Rd
flowStats/man/proBin.Rd
flowStats/man/quadrantGate.Rd
flowStats/man/rangeGate.Rd
flowStats/man/singletGate.Rd
flowStats/man/warpSet.Rd
flowStats/vignettes
flowStats/vignettes/GettingStartedWithFlowStats.Rnw