flowStats: Statistical methods for the analysis of flow cytometry data
Version 3.34.0

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

AuthorFlorian Hahne, Nishant Gopalakrishnan, Alireza Hadj Khodabakhshi, Chao-Jen Wong, Kyongryun Lee
Bioconductor views CellBasedAssays FlowCytometry
Date of publicationNone
MaintainerGreg Finak <gfinak@fhcrc.org> and Mike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version3.34.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowStats")

Getting started

Package overview

Popular man pages

BackGating: Sample backgating results
curv1Filter-class: Class "curv1Filter"
iProcrustes: Procrustes analysis. Using singular value decomposition (SVD)...
plotBins: Plots the probability bins overlaid with flowFrame data
proBin: Probability binning - a metric for evaluating multivariate...
quadrantGate: Automated quad gating
warpSet: Normalization based on landmark registration
See all...

All man pages Function index File listing

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

Functions

BackGating Man page
ITN Man page
SignifFeatureData Source code
SignifFeatureRegion Source code
\%in\%,flowFrame,curv1Filter-method Man page
\%in\%,flowFrame,curv2Filter-method Man page
\%in\%,flowFrame,lymphFilter-method Man page
\%in\%,flowFrame,rangeFilter-method Man page
area.in.polygon Source code
autoGate Man page Source code
backGating Source code
best.match Source code
binByRef Man page Source code
calcPBChiSquare Man page Source code
calcPearsonChi Man page Source code
calcReference Source code
centerFigure Source code
checkChannel Source code
checkFeatureNum Source code
choose.nk Source code
classifyFeatures Source code
combTransMatrix Source code
combinations.itr Source code
combinePols Source code
comparativeNormalizationPlot Source code
compute.confidence Source code
computeOverlap Source code
curv1Filter Man page Source code
curv1Filter-class Man page
curv2Filter Man page Source code
curv2Filter-class Man page
curvPeaks Man page Source code
curvRegs Source code
density1d Man page Source code
density1d_simple Source code
dfltBWrange Source code
dfltCounts Source code
drvkde Source code
extract.base.landmarks Source code
extract.landmarks Source code
extract.landmarksNC Source code
fdPar Source code
featureSignif Source code
filter.lms Source code
filterOutlier Source code
flowStats Man page
flowStats-package Man page
gateHasSufficientData Source code
gate_singlet Man page Source code
gau Source code
gaussNorm Man page Source code
gaussNormGS Source code
gaussNormNC Source code
getMinMaxRange Source code
getPeakRegions Source code
getProportions Source code
getRegions Source code
getSVD Source code
getSubsets Source code
getTranslationMatrix Source code
gpaSet Man page Source code
hdMat Source code
hubers1 Source code
iProcrustes Man page Source code
idFeatures Man page
idFeaturesByBackgating Man page Source code
landmarkMatrix Man page Source code
landmarkMatrixWithoutFilterResult Source code
landmarker Source code
lymphFilter Man page Source code
lymphFilter-class Man page
lymphGate Man page Source code
match.all.lms Source code
match.score Source code
normApprox Source code
normQA Man page Source code
normalize Man page
normalize,GatingSet,missing-method Man page
normalize,GatingSetInternal,missing-method Man page
normalize-methods Man page
normalize.one.expr Source code
normalize.one.exprNC Source code
normalizeGatingSet Source code
oneDGate Man page Source code
pcout Source code
peakSeparator Source code
plotAllGates Source code
plotBins Man page Source code
plotGPAprocess Source code
plotSameGate Source code
plotWorkFlow Source code
plotting Source code
print.GPA Source code
proBin Man page Source code
pruneRegions Source code
quadrantGate Man page Source code
rangeFilter Man page Source code
rangeFilter-class Man page
rangeGate Man page Source code
register.channel Source code
register.function Source code
remBoundary Source code
remBoundaryNC Source code
restoreBoundary Source code
restoreBoundaryNC Source code
returny Source code
rotateOnly Source code
score.lms Source code
show,curv1Filter-method Man page
show,curv2Filter-method Man page
simpleHd Source code
singletGate Man page
summarizeFilter,multipleFilterResult,curv1Filter-method Man page
summarizeFilter,multipleFilterResult,curv2Filter-method Man page
symconv.ks Source code
symconv2D.ks Source code
symconv3D.ks Source code
symconv4D.ks Source code
translate Source code
translateFeatures Source code
useDivCluster Source code
usingSVD Source code
warpSet Man page Source code
warpSetGS Man page Source code
warpSetNCDF Man page Source code
warpSetNCDFLowMem Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/autoGate.R
R/curvFilter-methods.R
R/curvPeaks.R
R/density1d.R
R/dfltCounts.R
R/drvkde.R
R/fda_functions.R
R/feature.R
R/gaussNorm.R
R/getPeakRegions.R
R/gpaSet.R
R/iProcrustes.R
R/idFeatures.R
R/landmarkMatrix.R
R/landmarkMatrixWithoutFilterResult.R
R/normalize-methods.R
R/pbin.R
R/pcout.R
R/peakSeparator.R
R/quadrantGate.R
R/singletGate.R
R/warpSet.R
build
build/vignette.rds
data
data/BackGating.rda
data/ITN.rda
data/datalist
inst
inst/doc
inst/doc/GettingStartedWithFlowStats.R
inst/doc/GettingStartedWithFlowStats.Rnw
inst/doc/GettingStartedWithFlowStats.pdf
man
man/BackGating.Rd
man/ITN.Rd
man/autoGate.Rd
man/binByRef.Rd
man/calcPBChiSquare.Rd
man/calcPearsonChi.Rd
man/curv1Filter-class.Rd
man/curv2Filter-class.Rd
man/curvPeaks.Rd
man/density1d.Rd
man/flowStats-package.Rd
man/gaussNorm.Rd
man/gpaSet.Rd
man/iProcrustes.Rd
man/idFeaturesByBackgating.Rd
man/landmarkMatrix.Rd
man/lymphGate.Rd
man/normQA.Rd
man/normalize.Rd
man/plotBins.Rd
man/proBin.Rd
man/quadrantGate.Rd
man/rangeGate.Rd
man/singletGate.Rd
man/warpSet.Rd
vignettes
vignettes/GettingStartedWithFlowStats.Rnw
flowStats documentation built on May 20, 2017, 10:41 p.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.