Bioconductor Task View: DNACopyNumber

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Package Maintainer Title
aCGH Jane Fridlyand Classes and functions for Array Comparative Genomic Hybridization data.
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
CGHbase Sjoerd Vosse CGHbase: Base functions and classes for arrayCGH data analysis.
CGHcall Sjoerd Vosse Calling aberrations for array CGH tumor profiles.
CGHregions Mark van de Wiel Dimension Reduction for Array CGH Data with Minimal Information Loss.
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
GLAD Philippe Hupe Gain and Loss Analysis of DNA
ITALICS Guillem Rigaill ITALICS
KCsmart Jorma de Ronde Multi sample aCGH analysis package using kernel convolution
MANOR Pierre Neuvial CGH Micro-Array NORmalization
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
reb Karl J. Dykema Regional Expression Biases
SIM Marten Boetzer Integrated Analysis of gene expression and copynumber data
SMAP Robin Andersson A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
snapCGH Thomas Hardcastle Segmentation, normalisation and processing of aCGH data.
SNPchip Robert Scharpf Classes and Methods for high throughput SNP chip data
VanillaICE Robert Scharpf Methods for fitting Hidden Markov Models to SNP chip data