CAFE: Chromosmal Aberrations Finder in Expression data

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Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input

Author
Sander Bollen
Date of publication
None
Maintainer
Sander Bollen <sander.h.bollen@gmail.com>
License
GPL-3
Version
1.10.0

View on Bioconductor

Man pages

armStats
Find aberrations with chromosome arm resolution
bandStats
Find aberrations with cytoband resolution
CAFE
CAFE data set
CAFE-package
Chromosomal Aberrations Finder in Expression data
chromosomeStats
Find aberrations with whole-chromosome resolution
cliSubset
Subset data with a CLI
discontPlot
Plot with discontinuous smoother
discontSmooth
A discontinuous smoother
facetPlot
Plot all chromosomes horizontally next to each other
fisher.method
Combines pvalues by using Fisher's method
guiSubset
Subset data with a GUI
ProcessCels
Processing CEL files
rawPlot
Plot without any smoother
slidPlot
Plot with sliding average smoother
slidSmooth
A moving average smoother

Files in this package

CAFE/DESCRIPTION
CAFE/NAMESPACE
CAFE/NEWS
CAFE/R
CAFE/R/chromosomeStats.R
CAFE/R/discontPlot.R
CAFE/R/facetPlot.R
CAFE/R/microProcess-improve.R
CAFE/R/rawPlot.R
CAFE/R/selectSamples.R
CAFE/R/slidPlot.R
CAFE/build
CAFE/build/vignette.rds
CAFE/data
CAFE/data/CAFE_data.RData
CAFE/data/datalist
CAFE/inst
CAFE/inst/doc
CAFE/inst/doc/CAFE-manual.R
CAFE/inst/doc/CAFE-manual.Rnw
CAFE/inst/doc/CAFE-manual.pdf
CAFE/inst/unitTests
CAFE/inst/unitTests/test_CAFE_ProcessCels.R
CAFE/inst/unitTests/test_CAFE_armStats.R
CAFE/inst/unitTests/test_CAFE_bandStats.R
CAFE/inst/unitTests/test_CAFE_chromosomeStats.R
CAFE/inst/unitTests/test_CAFE_cliSubset.R
CAFE/inst/unitTests/test_CAFE_discontPlot.R
CAFE/inst/unitTests/test_CAFE_discontSmooth.R
CAFE/inst/unitTests/test_CAFE_facetPlot.R
CAFE/inst/unitTests/test_CAFE_guiSubset.R
CAFE/inst/unitTests/test_CAFE_rawPlot.R
CAFE/inst/unitTests/test_CAFE_slidPlot.R
CAFE/inst/unitTests/test_CAFE_slidSmooth.R
CAFE/man
CAFE/man/CAFE-package.Rd
CAFE/man/CAFE.Rd
CAFE/man/ProcessCels.Rd
CAFE/man/armStats.Rd
CAFE/man/bandStats.Rd
CAFE/man/chromosomeStats.Rd
CAFE/man/cliSubset.Rd
CAFE/man/discontPlot.Rd
CAFE/man/discontSmooth.Rd
CAFE/man/facetPlot.Rd
CAFE/man/fisher.method.Rd
CAFE/man/guiSubset.Rd
CAFE/man/rawPlot.Rd
CAFE/man/slidPlot.Rd
CAFE/man/slidSmooth.Rd
CAFE/tests
CAFE/tests/runTests.R
CAFE/vignettes
CAFE/vignettes/CAFE-manual.Rnw
CAFE/vignettes/manual.bib
CAFE/vignettes/simple.png