flowPloidy: Analyze flow cytometer data to determine sample ploidy
Version 1.2.0

Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.

AuthorTyler Smith <tyler@plantarum.ca>
Bioconductor views FlowCytometry GUI Regression Visualization
Date of publicationNone
MaintainerTyler Smith <tyler@plantarum.ca>
LicenseGPL-3
Version1.2.0
URL https://github.com/plantarum/flowPloidy
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowPloidy")

Getting started

README.md
flowPloidy: Flow Cytometry Histograms
flowPloidy: Getting Started

Popular man pages

DebrisModels: Histogram Debris Models
fhAccessors: FlowHist Accessors
fhDoNLS: Fit the NLS model for a 'FlowHist' model
fhModels: Building Flow Histogram Models
FlowHist: FlowHist
FlowStandards: An S4 class to represent internal standard details for...
plot.FlowHist: Plot histograms for FlowHist objects
See all...

All man pages Function index File listing

Man pages

browseFlowHist: browseFlowHist
DebrisModels: Histogram Debris Models
fhAccessors: FlowHist Accessors
fhAnalyze: fhAnalyze
fhDoCounts: Calculcate 'FlowHist' nuclei counts
fhDoCV: Calculate CVs from a 'FlowHist' object
fhDoNLS: Fit the NLS model for a 'FlowHist' model
fhDoRCS: Calculate the Residual Chi-Square for a 'FlowHist' object
fhModels: Building Flow Histogram Models
fhStart: Calculate the where to start analysis for a 'FlowHist'...
findPeaks: findPeaks
FlowHist: FlowHist
flowPloidy: flowPloidy: A package for analyzing Flow Cytometry Histograms
FlowStandards: An S4 class to represent internal standard details for...
gauss: Gaussian model components
ModelComponent: An S4 class to represent model components
pickInit: Interactively select model starting values
plotFH: Plot the raw data for a FlowHist object
plot.FlowHist: Plot histograms for FlowHist objects
resetFlowHist: Reset the values in a 'FlowHist' object
setBins: setBins
setGate: setGate
tabulateFlowHist: exportFlowHist
updateFlowHist: updateFlowHist
viewFlowChannels: viewFlowChannels

Functions

DebrisModels Man page
FlowHist Man page Man page Source code
FlowStandards Man page Source code
GaussianComponents Man page
ModelComponent Man page Source code
MultipleCut Man page
PeakRatio Man page
RCS Man page
SingleCut Man page
addComponents Man page Source code
batchFlowHist Man page Source code
browseFlowHist Man page Source code
cleanPeaks Man page Source code
dropComponents Man page Source code
erf Source code
exFlowHist Source code
fhAccessors Man page
fhAnalyze Man page Source code
fhArgs Man page Source code
fhBins Man page Source code
fhCV Man page Source code
fhChannel Man page Source code
fhComps Man page Source code
fhCounts Man page Source code
fhDebris Man page Source code
fhDoCV Man page Source code
fhDoCounts Man page Source code
fhDoNLS Man page Source code
fhDoRCS Man page Source code
fhFile Man page Source code
fhGate Man page Source code
fhHistData Man page Source code
fhInit Man page Source code
fhLimits Man page Source code
fhLinearity Man page Source code
fhModel Man page Source code
fhModels Man page
fhNLS Man page Source code
fhOpts Man page Source code
fhPeaks Man page Source code
fhRCS Man page Source code
fhRaw Man page Source code
fhSamples Man page Source code
fhSpecialParams Man page Source code
fhStandards Man page Source code
fhStart Man page Source code
fhStdPeak Man page Source code
fhStdSelected Man page Source code
fhStdSizes Man page Source code
findPeaks Man page Source code
flowModels Man page
flowPloidy Man page
flowPloidy-package Man page
gauss Man page
getDoubletVals Source code
getInit Source code
getMultipleCutVals Man page Source code
getQuadrupletVals Source code
getSingleCutValsBase Man page Source code
getSpecialParamArgs Source code
getSpecialParams Source code
getSpecialParamsComp Source code
getTripletVals Source code
isGated Man page Source code
makeModel Man page Source code
mcColor Source code
mcDesc Source code
mcFunc Source code
mcIncludeTest Source code
mcInitParams Source code
mcName Source code
mcParamLimits Source code
mcSpecialParamSetter Source code
mcSpecialParams Source code
pickInit Man page Source code
pickPeaks Source code
plot.FlowHist Man page Source code
plotFH Man page Source code
plotGate Source code
plotResid Source code
resetFlowHist Man page Source code
selectPeaks Source code
setBins Man page Source code
setGate Man page Source code
setLimits Man page Source code
setLinearity Source code
stdPeak Man page Source code
stdSelected Man page Source code
stdSizes Man page Source code
tabulateFlowHist Man page Source code
updateFlowHist Man page Source code
viewFlowChannels Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/FlowHist.R
R/flowAnalysis.R
R/flowGate.R
R/flowPloidy.R
R/models.R
R/plotFlowHist.R
R/shiny.R
README.md
TODO.org
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/flowPloidy-gettingStarted.R
inst/doc/flowPloidy-gettingStarted.Rmd
inst/doc/flowPloidy-gettingStarted.html
inst/doc/histogram-tour.R
inst/doc/histogram-tour.Rmd
inst/doc/histogram-tour.html
man
man/DebrisModels.Rd
man/FlowHist.Rd
man/FlowStandards.Rd
man/ModelComponent.Rd
man/browseFlowHist.Rd
man/fhAccessors.Rd
man/fhAnalyze.Rd
man/fhDoCV.Rd
man/fhDoCounts.Rd
man/fhDoNLS.Rd
man/fhDoRCS.Rd
man/fhModels.Rd
man/fhStart.Rd
man/findPeaks.Rd
man/flowPloidy.Rd
man/gauss.Rd
man/pickInit.Rd
man/plot.FlowHist.Rd
man/plotFH.Rd
man/resetFlowHist.Rd
man/setBins.Rd
man/setGate.Rd
man/tabulateFlowHist.Rd
man/updateFlowHist.Rd
man/viewFlowChannels.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/testcore.R
tests/testthat/testmodels.R
vignettes
vignettes/draw_gate.png
vignettes/flowPloidy-gettingStarted.Rmd
vignettes/flowPloidy.bibtex
vignettes/flowShiny01.png
vignettes/flowShiny02.png
vignettes/flowShiny03.png
vignettes/flowShiny04.png
vignettes/flowShiny05.png
vignettes/flowShiny06.png
vignettes/flowShiny07.png
vignettes/fpPandoc.latex
vignettes/fw_high.png
vignettes/fw_low.png
vignettes/gate_ui.png
vignettes/gated_analysis.png
vignettes/gs_browse1.png
vignettes/gs_browse11.png
vignettes/gs_browse11b.png
vignettes/gs_browse11c.png
vignettes/gs_browse2.png
vignettes/gs_browse2c.png
vignettes/gs_browse3.png
vignettes/gs_browse3b.png
vignettes/gs_browse3c.png
vignettes/gs_gate.png
vignettes/gs_gate_zoom2.png
vignettes/histogram-tour.Rmd
vignettes/nw_high.png
vignettes/nw_low.png
vignettes/vac1.png
flowPloidy documentation built on May 20, 2017, 10:36 p.m.