flowStats: Statistical methods for the analysis of flow cytometry data

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
Date of publicationNone
MaintainerGreg Finak <gfinak@fhcrc.org> and Mike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version3.32.0

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

Functions

autoGate Man page
BackGating Man page
binByRef Man page
calcPBChiSquare Man page
calcPearsonChi Man page
curv1Filter Man page
curv1Filter-class Man page
curv2Filter Man page
curv2Filter-class Man page
curvPeaks Man page
density1d Man page
flowStats Man page
flowStats-package Man page
gaussNorm Man page
gpaSet Man page
idFeatures Man page
idFeaturesByBackgating Man page
\%in\%,flowFrame,curv1Filter-method Man page
\%in\%,flowFrame,curv2Filter-method Man page
\%in\%,flowFrame,lymphFilter-method Man page
\%in\%,flowFrame,rangeFilter-method Man page
iProcrustes Man page
ITN Man page
landmarkMatrix Man page
lymphFilter Man page
lymphFilter-class Man page
lymphGate Man page
normalize Man page
normalize,GatingSetInternal,missing-method Man page
normalize,GatingSet,missing-method Man page
normalize-methods Man page
normQA Man page
oneDGate Man page
plotBins Man page
proBin Man page
quadrantGate Man page
rangeFilter Man page
rangeFilter-class Man page
rangeGate Man page
show,curv1Filter-method Man page
show,curv2Filter-method Man page
singletGate Man page
summarizeFilter,multipleFilterResult,curv1Filter-method Man page
summarizeFilter,multipleFilterResult,curv2Filter-method Man page
warpSet Man page
warpSetGS Man page
warpSetNCDF Man page
warpSetNCDFLowMem Man page

Files

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

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

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

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