prada: Data analysis for cell-based functional assays

Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("prada")
AuthorFlorian Hahne <florian.hahne@novartis.com>, Wolfgang Huber <huber@ebi.ac.uk>, Markus Ruschhaupt, Joern Toedling <toedling@ebi.ac.uk>, Joseph Barry <joseph.barry@embl.de>
Bioconductor views CellBasedAssays Visualization
Date of publicationNone
MaintainerFlorian Hahne <florian.hahne@novartis.com>
LicenseLGPL
Version1.50.0

View on Bioconductor

Man pages

analysePlate: Apply a statistic to the data from each well in a plate

as.all: Coercion without introduction of NAs

barploterrbar: Barplot with error bars.

combineFrames: Combine the cytoFrames within a cytoSet according to some...

csApply: Apply a function over the intensities in a cytoSet

cytoFrame-class: 'cytoFrame': a class for storing observed quantitative...

cytoSet-class: 'cytoSet': a class for storing raw data from a quantitative...

data-cytoFrame: A sample cytoFrame object - German Cancer Research Center...

data-cytoSet: A sample cytoSet object - German Cancer Research Center...

devDims: Device Dimensions for plate plots

devRes: Resolution of current plotting device

fitNorm2: Fit bivariate normal distribution.

gate-class: 'gate': a class for subsetting flow-cytometry data by...

gateSet-class: 'gateSet': a class for subsetting flow-cytometry data by...

getAlphaNumeric: Convert from plate coordinates to alphanumeric notation.

getPradaPar: Set and query global parameters for functions in the prada...

new-internal: Internal functions called by other gating functions

plotNorm2: Plot fitted bivariate normal distribution.

plotPlate: Plot a well statistic for microtiter plates.

readCytoSet: Create a cytoSet object from one or more FCS 3.0 files

readFCS: Read an FCS file

readFCSaux: Auxiliary functions for readFCS

removeCensored: Remove rows that contain censored data

tcltkProgress: A simple tcltk progress window

threePanelPlot: Visualize cytometry data

thresholds: Discretize a two-dimensional data space into quadrants by...

touchFCS: Check for FCS files

vpLocation: Absolute location of current viewport

Functions

analysePlate Man page
appendGates Man page
appendGates,cytoFrame-method Man page
appendGates, gateSet_method Man page
appendGates,gateSet-method Man page
applyGate Man page
applyGate,cytoFrame,character-method Man page
applyGate,cytoFrame,gate-method Man page
applyGate,cytoFrame,gateSet-method Man page
applyGate,cytoFrame,logical-method Man page
applyGate,cytoFrame,numeric-method Man page
applyGate,matrix,gate-method Man page
applyGate,matrix,gateSet-method Man page
as.all Man page
as.gateSet Man page
as.gateSet,gate-method Man page
barploterrbar Man page
cframe Man page
colnames<-,cytoFrame-method Man page
colnames,cytoFrame-method Man page
colnames<-,cytoSet-method Man page
colnames,cytoSet-method Man page
combineFrames Man page
combineGates Man page
csApply Man page
cset Man page
cytoFrame Man page
$.cytoFrame Man page
[,cytoFrame,ANY,ANY,ANY-method Man page
cytoFrame-class Man page
cytoSet Man page
[[,cytoSet,ANY,missing-method Man page
[,cytoSet,ANY,missing,missing-method Man page
cytoSet-class Man page
[[<-,cytoSet-method Man page
description<-,cytoFrame,character-method Man page
description,cytoFrame-method Man page
devDims Man page
devRes Man page
drawGate Man page
drawGate,cytoFrame-method Man page
drawGate,matrix-method Man page
exprs<-,cytoFrame,matrix-method Man page
exprs,cytoFrame-method Man page
fitNorm2 Man page
gate Man page
gate<- Man page
gate-class Man page
gate<-,cytoFrame,gate-method Man page
gate<-,cytoFrame,gateSet-method Man page
gate,cytoFrame-method Man page
gatePoints Man page
gateSet Man page
[[,gateSet,ANY,missing-method Man page
[,gateSet,ANY,missing,missing-method Man page
gateSet-class Man page
getAlphaNumeric Man page
getPradaPar Man page
hist,cytoFrame-method Man page
hist,cytoSet-method Man page
killProgress Man page
length,cytoSet-method Man page
length,gateSet-method Man page
lines,gate-method Man page
names<-,gate-method Man page
names,gate-method Man page
names<-,gateSet-method Man page
names,gateSet-method Man page
ncol,cytoFrame-method Man page
nrow,cytoFrame-method Man page
pData,cytoSet-method Man page
phenoData<-,cytoSet,AnnotatedDataFrame-method Man page
phenoData,cytoSet-method Man page
plot,cytoFrame,missing-method Man page
plot,cytoSet,missing-method Man page
plotNorm2 Man page
plotPlate Man page
progress Man page
readCytoSet Man page
read.fcs Man page
readFCS Man page
readFCSdata Man page
readFCSgetPar Man page
readFCSheader Man page
readFCStext Man page
removeCensored Man page
removeCensored,cytoFrame-method Man page
removeCensored,data.frame-method Man page
removeCensored,matrix-method Man page
setPradaPars Man page
show,cytoFrame-method Man page
show,cytoSet-method Man page
show,gate-method Man page
show,gateSet-method Man page
split,cytoSet,ANY,ANY-method Man page
split,cytoSet,ANY-method Man page
split,cytoSet-method Man page
threePanelPlot Man page
thresholds Man page
touchFCS Man page
updateProgress Man page
vpLocation Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/analysePlate.R R/as.all.R R/barploterrbar.R R/combineFrames.R R/combineGates.R R/csApply.R R/cytoFunctions.R R/fitNorm2.R R/gateMatrix.R R/getAlphanumeric.R R/getPradaPar.R R/methods-cytoFrame.R R/methods-cytoSet.R R/methods-gate.R R/methods-gateSet.R R/methods-misc.R R/plotNorm2.R R/plotPlate.R R/readCytoSet.R R/readFCS.R R/readSDM.R R/removeCensored.R R/tcltkProgress.R R/thresholds.R R/touchFCS.R
build
build/vignette.rds
data
data/cframe.rda
data/cset.rda
inst
inst/doc
inst/doc/norm2.R
inst/doc/norm2.Rnw
inst/doc/norm2.pdf
inst/doc/prada2cellHTS.R
inst/doc/prada2cellHTS.Rnw
inst/doc/prada2cellHTS.pdf
inst/extdata
inst/extdata/Description.txt
inst/extdata/Experiment1.txt
inst/extdata/Experiment2.txt
inst/extdata/GeneIDs.txt
inst/extdata/Plateconf.txt
inst/extdata/Platelist.txt
inst/extdata/Screenlog.txt
inst/extdata/dorit13_2c-1-2--13-Ytrail=3143937171.xml
inst/extdata/fas-Bcl2-plate323-04-04.A01
inst/extdata/fas-Bcl2-plate323-04-04.A02
inst/extdata/fas-Bcl2-plate323-04-04.A03
inst/extdata/fas-Bcl2-plate323-04-04.B01
inst/extdata/fas-Bcl2-plate323-04-04.B02
inst/extdata/fas-Bcl2-plate323-04-04.B03
inst/extdata/plate3_1.txt
inst/extdata/plate3_2.txt
inst/extdata/plate3_3.txt
inst/extdata/plate4_1.txt
inst/extdata/plate4_2.txt
inst/extdata/plate4_3.txt
inst/extdata/sampleData.txt
man
man/analysePlate.Rd man/as.all.Rd man/barploterrbar.Rd man/combineFrames.Rd man/csApply.Rd man/cytoFrame-class.Rd man/cytoSet-class.Rd man/data-cytoFrame.Rd man/data-cytoSet.Rd man/devDims.Rd man/devRes.Rd man/fitNorm2.Rd man/gate-class.Rd man/gateSet-class.Rd man/getAlphaNumeric.Rd man/getPradaPar.Rd man/new-internal.Rd man/plotNorm2.Rd man/plotPlate.Rd man/readCytoSet.Rd man/readFCS.Rd man/readFCSaux.Rd man/removeCensored.Rd man/tcltkProgress.Rd man/threePanelPlot.Rd man/thresholds.Rd man/touchFCS.Rd man/vpLocation.Rd
src
src/inPolygon.c
vignettes
vignettes/fcs3.html
vignettes/norm2.Rnw
vignettes/prada2cellHTS.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.