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

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

Author
Errol Strain, Florian Hahne, and Perry Haaland
Date of publication
None
Maintainer
Errol Strain <estrain@gmail.com>
License
Artistic-2.0
Version
1.32.0
URLs

View on Bioconductor

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.

Files in this package

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