MANOR: CGH Micro-Array NORmalization

Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MANOR")
AuthorPierre Neuvial <pierre.neuvial@genopole.cnrs.fr>, Philippe Hupe <philippe.hupe@curie.fr>
Bioconductor views CopyNumberVariation DataImport Microarray Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerPierre Neuvial <pierre.neuvial@genopole.cnrs.fr>
LicenseGPL-2
Version1.46.0
http://bioinfo.curie.fr/projects/manor/index.html

View on Bioconductor

Functions

add.lines Man page
amplicon.flag Man page
arrayCGH2txt Man page
arrayTrend Man page
arrayTrend.arrayCGH Man page
arrayTrend.default Man page
center Man page
check.names Man page
chrom Man page
chromosome.flag Man page
clone.qscore Man page
control.flag Man page
cv Man page
dapi.snr.flag Man page
detectSB Man page
detectSB.arrayCGH Man page
detectSB.default Man page
dynamics.qscore Man page
dyn.x.qscore Man page
dyn.y.qscore Man page
edge Man page
edge.norm Man page
edge.txt Man page
flag Man page
flag.aggregate.arrayCGH Man page
flag.arrayCGH Man page
flags Man page
flag.summary Man page
flag.summary.arrayCGH Man page
flag.summary.default Man page
genome.plot Man page
genome.plot.arrayCGH Man page
genome.plot.default Man page
getChromosomeArm Man page
global.spatial.flag Man page
gradient Man page
gradient.gpr Man page
gradient.norm Man page
html.report Man page
html.report.arrayCGH Man page
html.report.default Man page
import Man page
import.default.aux Man page
import.gpr.aux Man page
import.spot.aux Man page
intensity.flag Man page
intensity.plot Man page
local.spatial.flag Man page
manor Man page
MANOR Man page
MANOR-internal Man page
my.aggregate.data.frame Man page
nem Man page
nem.arrayCGH Man page
nem.default Man page
norm Man page
norm.arrayCGH Man page
num.chromosome.flag Man page
pct.clone.qscore Man page
pct.replicate.qscore Man page
pct.spot.before.qscore Man page
pct.spot.qscore Man page
position.flag Man page
print.flag Man page
qscore Man page
qscore.arrayCGH Man page
qscore.summary Man page
qscore.summary.arrayCGH Man page
ref.snr.flag Man page
rename Man page
rep.flag Man page
replicate.aux Man page
replicate.flag Man page
report.plot Man page
report.plot.arrayCGH Man page
report.plot.default Man page
smoothness.qscore Man page
SNR.flag Man page
sort Man page
sort.arrayCGH Man page
spatial Man page
spatial.flag Man page
spot.corr.flag Man page
spot.flag Man page
to.flag Man page
to.qscore Man page
unique.flag Man page
val.mark.flag Man page
var.replicate.qscore Man page
w Man page

Files

DESCRIPTION
NAMESPACE
R
R/arrayCGH2txt.R R/arrayTrend.R R/detectSB.R R/flag.arrayCGH.R R/flag.summary.R R/genome.plot.R R/html.report.R R/import.R R/intensity.plot.R R/nem.R R/norm.R R/quality.R R/report.plot.R R/sort.R R/to.flag.R R/utils.R
build
build/vignette.rds
data
data/flags.RData
data/qscores.RData
data/spatial.RData
inst
inst/NEWS
inst/doc
inst/doc/MANOR.R
inst/doc/MANOR.Rnw
inst/doc/MANOR.pdf
inst/extdata
inst/extdata/edge.txt
inst/extdata/gradient.gpr
inst/system
inst/system/checkDataObjects.R
man
man/MANOR-internal.Rd man/arrayTrend.Rd man/detectSB.Rd man/flag.arrayCGH.Rd man/flag.summary.Rd man/flags.Rd man/genome.plot.Rd man/html.report.Rd man/import.Rd man/nem.Rd man/norm.Rd man/qscore.Rd man/qscore.arrayCGH.Rd man/qscore.summary.Rd man/qscores.Rd man/report.plot.Rd man/sort.Rd man/spatial.Rd man/to.flag.Rd
src
src/Rnem_arg.c
src/Rnem_exe.c
src/exememo.c
src/genmemo.h
src/nem_alg.c
src/nem_alg.h
src/nem_arg.h
src/nem_hlp.c
src/nem_hlp.h
src/nem_mod.c
src/nem_mod.h
src/nem_nei.c
src/nem_nei.h
src/nem_rnd.c
src/nem_rnd.h
src/nem_typ.h
src/nem_ver.c
src/nem_ver.h
vignettes
vignettes/MANOR.Rnw
vignettes/MANOR.bib
vignettes/html.sty
vignettes/index.html
vignettes/natbib.sty

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