Package: ADaCGH2 2.45.0

Ramon Diaz-Uriarte

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, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Authors:Ramon Diaz-Uriarte <[email protected]> and Oscar M. Rueda <[email protected]>. Wavelet-based aCGH smoothing code from Li Hsu <[email protected]> and Douglas Grove <[email protected]>. Imagemap code from Barry Rowlingson <[email protected]>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>. Code from ffbase <https://github.com/edwindj/ffbase> by Edwin de Jonge <[email protected]>, Jan Wijffels, Jan van der Laan.

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Bug tracker:https://github.com/rdiaz02/adacgh2/issues

On BioConductor:ADaCGH2-2.45.0(bioc 3.20)ADaCGH2-2.44.0(bioc 3.19)

bioconductor-package

10 exports 1.00 score 89 dependencies

Last updated 2 months agofrom:3db9be4050

Exports:cutFileinputToADaCGHoutputToCGHregionspChromPlotpSegmentCGHsegpSegmentDNAcopypSegmentGLADpSegmentHaarSegpSegmentHMMpSegmentWavelets

Dependencies:aCGHaffyaffyioannotateAnnotationDbiaskpassawsawsMethodsBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemcliclustercolorspacecpp11crayoncurlDBIDNAcopyfansifarverfastmapffgenefilterGenomeInfoDbGenomeInfoDbDataggplot2GLADgluegslgtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemultitapermulttestmunsellnlmeopensslpillarpixmappkgconfigplogrpngpreprocessCoreR6RColorBrewerrlangRSQLiteS4VectorssandwichscalesstatmodstrucchangesurvivalsystibbletilingArrayUCSC.utilsutf8vctrsviridisLitevsnwaveslimwithrXMLxtableXVectorzlibbioczoo