GLAD: Gain and Loss Analysis of DNA

Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GLAD")
AuthorPhilippe Hupe
Bioconductor views CopyNumberVariation Microarray
Date of publicationNone
MaintainerPhilippe Hupe <glad@curie.fr>
LicenseGPL-2
Version2.38.0
http://bioinfo.curie.fr

View on Bioconductor

Functions

affectationGNL Man page
affectationGNL.profileCGH Man page
array1 Man page
array2 Man page
array3 Man page
arrayCGH Man page
arrayPersp Man page
arrayPersp.arrayCGH Man page
arrayPersp.default Man page
arrayPlot Man page
arrayPlot.arrayCGH Man page
arrayPlot.default Man page
as.data.frame.profileCGH Man page
as.profileCGH Man page
as.profileCGH.data.frame Man page
BkpInfo Man page
BkpInfo.profileCGH Man page
CheckData Man page
CheckData.profileCGH Man page
chrBreakpoints Man page
chrBreakpoints.profileCGH Man page
ChrNumeric Man page
cluster Man page
clusterglad Man page
clusterglad.hclust Man page
ColorBar Man page
cytoband Man page
daglad Man page
daglad.profileCGH Man page
DelRegionTooSmall Man page
detectOutliers Man page
detectOutliers.profileChr Man page
dogenomestep Man page
FDRThres Man page
filterBkp Man page
filterBkp.profileCGH Man page
filterBkpStep Man page
filterBkpStep.profileCGH Man page
findCluster Man page
findCluster.profileChr Man page
glad Man page
GLAD-internal Man page
glad.profileCGH Man page
gm00143 Man page
gm01524 Man page
gm01535 Man page
gm01750 Man page
gm02948 Man page
gm03134 Man page
gm03563 Man page
gm03576 Man page
gm04435 Man page
gm05296 Man page
gm07081 Man page
gm07408 Man page
gm10315 Man page
gm13031 Man page
gm13330 Man page
HaarSeg Man page
HaarSegGLAD Man page
HaarSegGLADCPP Man page
hclustglad Man page
kernelpen Man page
lawsglad Man page
loopRemove Man page
loopRemove.profileChr Man page
MoveBkp Man page
MoveBkp.profileCGH Man page
MoveBkpStep Man page
MoveBkpStep.profileCGH Man page
myPalette Man page
OptimBkpFindCluster Man page
OutliersGNL Man page
OutliersGNL.profileCGH Man page
P20 Man page
P9 Man page
plotCytoBand Man page
plotCytoBand.default Man page
plotProfile Man page
plotProfile.profileCGH Man page
prepare.output.daglad Man page
profileCGH Man page
profileChr Man page
RecomputeGNL Man page
removeBreakpoints Man page
removeBreakpoints.profileChr Man page
removeLevel Man page
removeLevel.profileChr Man page
SegmentByPeaks Man page
selectindex Man page
testBkpToMove Man page
testBkpToMove.profileCGH Man page
tkdaglad Man page
tkdaglad.default Man page
tkglad Man page
tkglad.default Man page

Files

CHANGELOG
DESCRIPTION
NAMESPACE
R
R/BkpInfo.R R/CheckData.R R/ChrNumeric.R R/HaarSeg.R R/MoveBkp.R R/MoveBkpStep.R R/OutliersGNL.R R/affectationGNL.R R/arrayPlot.R R/as.profileCGH.R R/chrBreakpoints.R R/daglad.R R/detectOutliers.R R/filterBkp.R R/filterBkpStep.R R/findCluster.R R/glad.R R/hclust.R R/kernel.R R/laws-glad.R R/loopRemove.R R/plotCytoBand.R R/plotProfile.R R/tkdaglad.R R/tkglad.R R/zzz.R
aclocal.m4
build
build/vignette.rds
cleanup
configure
configure.ac
configure.ac.old
data
data/arrayCGH.RData
data/cytoband.RData
data/snijders.RData
data/veltman.RData
demo
demo/00Index
demo/tkdaglad.R demo/tkglad.R
inst
inst/README
inst/doc
inst/doc/GLAD.R
inst/doc/GLAD.Rnw
inst/doc/GLAD.pdf
man
man/ChrNumeric.Rd man/ColorBar.Rd man/GLAD-internal.Rd man/arrayCGH.Rd man/arrayPersp.Rd man/arrayPlot.Rd man/as.data.frame.profileCGH.Rd man/as.profileCGH.Rd man/bladder.Rd man/cytoband.Rd man/daglad.Rd man/glad.Rd man/hclust.Rd man/kernel.Rd man/myPalette.Rd man/plotProfile.Rd man/profileCGH.Rd man/snijders.Rd man/tkdaglad.Rd man/veltman.Rd
src
src/BkpInfo.cpp
src/HaarSeg.cpp
src/HaarSeg.h
src/Makevars.in
src/Makevars.win
src/MoveBkp.cpp
src/MoveBkp.h
src/OutliersGNL.cpp
src/chrBreakpoints.cpp
src/chrBreakpoints.h
src/cutree.cpp
src/cutree.h
src/daglad.cpp
src/distance.cpp
src/filterBkp.cpp
src/filterBkp.h
src/findCluster.cpp
src/findCluster.h
src/glad-limits.h
src/glad-struct.h
src/glad-utils.cpp
src/glad-utils.h
src/hclust.cpp
src/laws.c
src/laws.h
src/loopRemove.cpp
src/loopRemove.h
src/mva.h
vignettes
vignettes/GLAD.Rnw
vignettes/biblio.bib

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