Bioconductor Task View: CopyNumberVariants

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Package Maintainer Title
aCGH Peter Dimitrov Classes and functions for Array Comparative Genomic Hybridization data.
ADaCGH2 Ramon Diaz-Uriarte Analysis of data from aCGH experiments using parallel computing and ff objects
beadarraySNP Jan Oosting Normalization and reporting of Illumina SNP bead arrays
CGHbase Sjoerd Vosse CGHbase: Base functions and classes for arrayCGH data analysis.
cghMCR J. Zhang Find chromosome regions showing common gains/losses
CGHregions Sjoerd Vosse Dimension Reduction for Array CGH Data with Minimal Information Loss.
Clonality Irina Ostrovnaya Clonality testing
cn.farms Andreas Mitterecker , Djork-Arne Clevert cn.farms - Factor Analysis for copy number estimation
CNTools J. Zhang Convert segment data into a region by sample matrix to allow for other high level computational analyses.
crlmm Benilton S Carvalho , Robert Scharpf , Matt Ritchie Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
DNAcopy Venkatraman E. Seshan DNA copy number data analysis
GLAD Philippe Hupe Gain and Loss Analysis of DNA
ITALICS Guillem Rigaill ITALICS
MANOR Pierre Neuvial CGH Micro-Array NORmalization
mBPCR P.M.V. Rancoita Bayesian Piecewise Constant Regression for DNA copy number estimation
oligo Benilton Carvalho Preprocessing tools for oligonucleotide arrays.
quantsmooth Jan Oosting Quantile smoothing and genomic visualization of array data
reb Karl J. Dykema Regional Expression Biases
SMAP Robin Andersson A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
snapCGH John Marioni Segmentation, normalisation and processing of aCGH data.
SNPchip Robert Scharpf Classes and Methods for high throughput SNP chip data
VanillaICE Robert Scharpf A Hidden Markov Model for high throughput genotyping arrays