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).

Author
Florian 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>
Date of publication
None
Maintainer
Florian Hahne <florian.hahne@novartis.com>
License
LGPL
Version
1.50.0

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

Files in this package

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