Table 1 Software for array CGH analysis

CGH Fusion

Cost

L, W

Java

Lowess normalisation, CBS, ratio thresholding

http://www.infoquant.com/index/cghfusion

Agilent Genomic

Workbench Standard

Edition 5.0.14

Cost

L, W

Java

UCSC Genome Browser

http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnaanalyticssoftware/pages/default.aspx

Cluster multiple samples into groups based on their aberration profiles

Hidden Markov model (HMM) for detecting probe-based aberrations

Circular binary segmentation (CBS)

infoQuant

oneClickCGH

Cost

L, W

CBS-type algorithms, log-ratio thresholding etc

http://www.infoquant.com/index/oneclickcgh

CNAM

Cost

L, W, M

Univariate

http://www.goldenhelix.com/SNP_Variation/CNAM/index.html

Multivariate

CytoSure

Cost

L, W, M

Direct thresholding, moving average thresholding,

K-means clustering, HMM and CBS

http://www.ogt.co.uk/analysis_software.html

CNV workshop

Free

L, W, M

Java, R, Perl

CBS segmentation algorithm

http://sourceforge.net/projects/cnv

Log ratio for normalisation

SnoopCGH

Free

L, W, M

Java

Haar wavelets

http://snoopcgh.sourceforge.net/

Smith-Waterman algorithm

permutations

PennCNV

Free

L, W

HMM

QuantiSNP

Free

L, W

MATLAB

Linux user

(glibc2.6+)

Objective Bayes HMM (OB-HMM)

http://www.well.ox.ac.uk/QuantiSNP/

Ultrasome

Free

L, W

Stand-alone

program

http://www.broadinstitute.org/ultrasome

CGHExplorer

Free

L, W, M

J2SEJRE

Thresholding, bootstrap-based method, analysis of copy errors (ACE), clustering along chromosomes

(CALC) with false discovery rate (FDR)

http://www.ifi.uio.no/forskning/grupper/bioinf/Papers/CGH/

CGHPRO

Free

L, W

Java

Quantile smoothing

http://www.mcu.edu.tw/department/biotec/en_page/CGcgh/

My SQL

Wavelet-based smoothing

RJaCGH

Free

L, W, M

R

HMM

http://cran.r-project.org/web/packages/RJaCGH/index.html

ADaCGH

Free

L, W, M

R

CBS, HMM, BioHMM, comparative genomic hybridisation (CGH) segmentation, gain and loss analysis of DNA

(GLAD), wavelet-based smoothing, Smith-Waterman

algorithm and analysis of copy errors

http://cran.r-project.org/web/packages/ADaCGH/

Web-based

CLAC

Free

L, W, M

R

Clustering along chromosomes

http://cran.r-project.org/src/contrib/Archive/clac

CGHseg

Free

L, W, M

R

CGH segmentation

ISACGH

Free

L, W, M

Web based

GLAD, CBS

Fisher's exact test

GO, KEGG pathway

http://www.gepas.org

aCGH

Free

L, W, M

R

HMM

GLAD

Free

L, W, M

R

Gaussian-based likelihood

http://www.bioconductor.org/packages/2.1/bioc/html/GLAD.html

Adaptive weights smoothing

CBS

Free

L, W, M

R

CBS

CBS algorithm has been implemented in the 'DNAcopy' package

DNAcopy

Free

L, W, M

R

CBS

http://www.bioconductor.org/packages/2.0/bioc/html/DNAcopy.html

snapCGH

Free

L, W, M

R

Limma, GLAD, DNAcopy, tilingArray and aCGH

http://www.bioconductor.org/packages/1.9/bioc/html/snapCGH.html

CGHcall

Free

L, W, M

R

Expectation maximisation (EM)

http://www.bioconductor.org/packages/release/bioc/html/CGHcall.html

cghMCR

Free

L, W, M

R

DNAcopy

http://www.bioconductor.org/packages/bioc/html/cghMCR.html

Minimal common regions (MCRs)

BioHMM

Free

L, W, M

R

Heterogeneous HMM

http://www.bioconductor.org/packages/bioc/1.8/html/snapCGH.html

fused lasso

Free

L, W, M

R

Regression

http://cran.r-project.org/web/packages/cghFLasso/

aroma.affymetrix

Free

L, W, M

R

GLAD

http://www.aroma-project.org/

ChromosomeExplorer