| 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 |