ADaCGH2: Analysis of big data from aCGH experiments using parallel computing and ff objects

Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ADaCGH2")
AuthorRamon Diaz-Uriarte <rdiaz02@gmail.com> and Oscar M. Rueda <rueda.om@gmail.com>. Wavelet-based aCGH smoothing code from Li Hsu <lih@fhcrc.org> and Douglas Grove <dgrove@fhcrc.org>. Imagemap code from Barry Rowlingson <B.Rowlingson@lancaster.ac.uk>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>.
Bioconductor views CopyNumberVariants Microarray
Date of publicationNone
MaintainerRamon Diaz-Uriarte <rdiaz02@gmail.com>
LicenseGPL (>= 3)
Version2.14.0
https://github.com/rdiaz02/adacgh2

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/ADaCGH-2.R R/HaarSeg.R R/imagemap.R
README.code.authors
build
build/vignette.rds
data
data/inputEx-sp.txt
data/inputEx.RData
data/inputEx.txt
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ADaCGH2-long-examples.pdf
inst/doc/ADaCGH2.R
inst/doc/ADaCGH2.Rnw
inst/doc/ADaCGH2.pdf
inst/doc/benchmarks.pdf
inst/doc/index.html
inst/example-datadir
inst/example-datadir/Chrom.txt
inst/example-datadir/ID.txt
inst/example-datadir/Pos.txt
inst/example-datadir/col_4.txt
inst/example-datadir/col_5.txt
inst/example-datadir/col_6.txt
inst/example-datadir/col_7.txt
inst/example-datadir/col_8.txt
inst/example-datadir/col_9.txt
inst/imagemap-example
inst/imagemap-example/README-usage-Python-for-HTML-with-maps.txt
inst/imagemap-example/toMap.py
inst/imagemap-example/toMapMod.py
inst/sources-tex-Rnw-other
inst/sources-tex-Rnw-other/ADaCGH2-long-examples.R
inst/sources-tex-Rnw-other/ADaCGH2-long-examples.Rnw
inst/sources-tex-Rnw-other/README-sources-tex-Rnw-other
inst/sources-tex-Rnw-other/anal-benchmark-fig.pdf
inst/sources-tex-Rnw-other/anal-coleonyx.tex
inst/sources-tex-Rnw-other/anal-gallotia.tex
inst/sources-tex-Rnw-other/anal-lacerta-gallotia.tex
inst/sources-tex-Rnw-other/anal-lacerta.tex
inst/sources-tex-Rnw-other/benchmarks.bib
inst/sources-tex-Rnw-other/benchmarks.tex
inst/sources-tex-Rnw-other/read-coleonyx.tex
inst/sources-tex-Rnw-other/read-gallotia.tex
inst/sources-tex-Rnw-other/read-lacerta.tex
inst/sources-tex-Rnw-other/reading-benchmark-fig.pdf
man
man/cutFile.Rd man/inputEx.Rd man/inputToADaCGH.Rd man/outputToCGHregions.Rd man/pChromPlot.Rd man/pSegment.Rd
src
src/all_headers.h
src/init.c
src/r_haarseg.c
vignettes
vignettes/ADaCGH2.Rnw
vignettes/ADaCGH2.bib

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