plateCore: Statistical tools and data structures for plate-based flow cytometry
Version 1.34.0

Provides basic S4 data structures and routines for analyzing plate based flow cytometry data.

Browse man pages Browse package API and functions Browse package files

AuthorErrol Strain, Florian Hahne, and Perry Haaland
Bioconductor views CellBasedAssays FlowCytometry Infrastructure
Date of publicationNone
MaintainerErrol Strain <estrain@gmail.com>
LicenseArtistic-2.0
Version1.34.0
URL http://www.bioconductor.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("plateCore")

Man pages

applyControlGates-methods: Apply control gates to a flowPlate
compensate-methods: Compensate a flowPlate to correct for the effects of...
compensationSet: Sample Compensation Data Set
densityplot-methods: One-dimensional density plots for flowPlates
fixAutoFl-methods: Correct for the effects of cell size (FSC) on...
flowPlate-class: The flowPlate class.
flowPlate-method: Create a flowPlate
fpbind-methods: Merge multiple flowPlates into a single virtual flowPlate
getGroups-methods: Retrieve Negative control groups from a flowPlate
gutterPlot-methods: gutterPlot
mfiPlot-methods: mfiPlot
on-methods: Methods for Function %on% in Package 'plateCore'
panel.densityplot.flowPlate: Lattice-flowViz style panel function for flowPlate...
panel.xyplot.flowPlate: Lattice-flowViz style panel function for flowPlate xyplot.
pbmcPlate: pbmcPlate Data Set
plateCore-package: plateCore: A Bioconductor package for high throughput...
plateSet-methods: Get the flowSet from a flowPlate object
plotPlate-methods: plotPlate
prepanel.densityplot.flowPlate: Lattice-flowViz style panel function for flowPlate...
prepanel.xyplot.flowPlate: Lattice-flowViz style panel function for flowPlate xyplot.
setControlGates-methods: Create control gates for a flowPlate
Subset-methods: Subset
summaryStats-methods: Compute summary statistics on a flowPlate
wellAnnotation-methods: Retrieve a data.frame describing the content of a flowPlate
xyplot-methods: Scatter plots (dotplots) for flowPlates.

Functions

Subset Man page
Subset,flowPlate,ANY-method Man page
Subset,flowPlate-method Man page
Subset-method Man page
[,flowPlate,ANY-method Man page
[[,flowPlate,ANY-method Man page
\%on\% Man page
\%on\%,ANY,flowPlate-method Man page
\%on\%-methods Man page
applyControlGates Man page
applyControlGates,flowPlate-method Man page
applyControlGates-methods Man page
colorramp Source code
compensate Man page
compensate,flowPlate,ANY-method Man page
compensate-method Man page
compensationSet Man page
createUniqueColumnName Source code
densityplot Man page
densityplot,formula,flowPlate,ANY,ANY,ANY,missing-method Man page
densityplot,formula,flowPlate-method Man page
densityplot-method Man page
evalInFlowFrame Source code
expr2char Source code
fixAutoFl Man page
fixAutoFl,flowPlate-method Man page
fixAutoFl-method Man page
flowPhenoMerge Source code
flowPlate Man page
flowPlate,flowSet-method Man page
flowPlate-class Man page
flowPlate-method Man page
fpbind Man page
fpbind,flowPlate,flowPlate-method Man page
fpbind-method Man page
getGroups Man page
getGroups,flowPlate-method Man page
getGroups-method Man page
gutterPlot Man page
gutterPlot,flowPlate-method Man page
gutterPlot-method Man page
makePlateLayout Source code
manipulate.call Source code
mfiPlot Man page
mfiPlot,flowPlate-method Man page
mfiPlot-method Man page
panel.densityplot.flowPlate Man page Source code
panel.xyplot.flowPlate Man page Source code
pbmcPlate Man page
phenoData,flowPlate-method Man page
plateCore Man page
plateCore-package Man page
plateSet Man page
plateSet,flowPlate-method Man page
plateSet-method Man page
plotPlate Man page
plotPlate,flowPlate-method Man page
plotPlate-method Man page
prepanel.densityplot.flowPlate Man page Source code
prepanel.xyplot.flowPlate Man page Source code
sampleNames,flowPlate-method Man page
setControlGates Man page
setControlGates,flowPlate-method Man page
setControlGates-method Man page
summaryStats Man page
summaryStats,flowPlate-method Man page
summaryStats-method Man page
wellAnnotation Man page
wellAnnotation,flowPlate-method Man page
wellAnnotation-method Man page
xyplot Man page
xyplot,formula,flowPlate-method Man page
xyplot-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/densityplotFlowPlate.R
R/flowPlate-accessors.R
R/flowPlate-plotting.R
R/flowPlate-utilities.R
R/utilities.R
R/xyplotFlowPlate.R
build
build/vignette.rds
data
data/plateCore.rda
inst
inst/doc
inst/doc/plateCoreVig.R
inst/doc/plateCoreVig.Rnw
inst/doc/plateCoreVig.pdf
man
man/Subset-methods.Rd
man/applyControlGates-methods.Rd
man/compensate-methods.Rd
man/compensationSet.Rd
man/densityplot-methods.Rd
man/fixAutoFl-methods.Rd
man/flowPlate-class.Rd
man/flowPlate-method.Rd
man/fpbind-methods.Rd
man/getGroups-methods.Rd
man/gutterPlot-methods.Rd
man/mfiPlot-methods.Rd
man/on-methods.Rd
man/panel.densityplot.flowPlate.Rd
man/panel.xyplot.flowPlate.Rd
man/pbmcPlate.Rd
man/plateCore-package.Rd
man/plateSet-methods.Rd
man/plotPlate-methods.Rd
man/prepanel.densityplot.flowPlate.Rd
man/prepanel.xyplot.flowPlate.Rd
man/setControlGates-methods.Rd
man/summaryStats-methods.Rd
man/wellAnnotation-methods.Rd
man/xyplot-methods.Rd
paper
paper/EdResponse.doc
paper/ResponseToReviewers.doc
paper/ResponseToReviewers.pdf
paper/analysisSteps.odg
paper/analysisSteps.pdf
paper/bioconductorReview.txt
paper/fjVSr.emf
paper/fjVSr.pdf
paper/fjVSr.svg
paper/fjVSr2.svg
paper/fjVSr3.pdf
paper/fjVSrDf.csv
paper/isoplot.pdf
paper/isoplot.svg
paper/mfiRatio.pdf
paper/mfiRatio.svg
paper/mfiRatio2.pdf
paper/mfiRatio2.svg
paper/mfiRatioB.pdf
paper/outline.aux
paper/outline.bbl
paper/outline.bib
paper/outline.blg
paper/outline.tex
paper/outlineOLD.Rnw
paper/percentagesRandFJ.csv
paper/plateCore.doc
paper/plateCoreReviewer1.doc
paper/plateCoreReviewer2.doc
paper/rVSfjByFL.emf
paper/rVSfjByFL.pdf
paper/rVSfjByFL.svg
paper/replicate.emf
paper/replicate.pdf
paper/replicate.svg
vignettes
vignettes/expDens.pdf
vignettes/plateCoreVig.Rnw
plateCore documentation built on May 20, 2017, 9:41 p.m.