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.

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>.
Date of publicationNone
MaintainerRamon Diaz-Uriarte <rdiaz02@gmail.com>
LicenseGPL (>= 3)
Version2.14.0
https://github.com/rdiaz02/adacgh2

View on Bioconductor

Files in this package

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

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