ADaCGH statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ADaCGH
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Protocols

ADaCGH specifications

Information


Unique identifier OMICS_00700
Name ADaCGH
Alternative name Analysis of Data from aCGH
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ramón Diaz-Uriarte

Information


Unique identifier OMICS_00700
Name ADaCGH
Alternative name Analysis of Data from aCGH
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ramón Diaz-Uriarte

Publications for Analysis of Data from aCGH

ADaCGH citations

 (7)
library_books

Autoregressive Higher Order Hidden Markov Models: Exploiting Local Chromosomal Dependencies in the Analysis of Tumor Expression Profiles

2014
PLoS One
PMCID: 4067306
PMID: 24955771
DOI: 10.1371/journal.pone.0100295

[…] mely fast requiring only 11 seconds. However, the AR()-HMM() with a fourth-order emission process and a second-order state-transition process had nearly the same runtime as GLAD, which was run on the ADaCGH web-server utilizing parallel computations. To further evaluate all different methods, we subsequently study how the more complex modeling of local chromosomal dependencies by autoregressive hi […]

call_split

Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome

2012
PLoS One
PMCID: 3368837
PMID: 22701658
DOI: 10.1371/journal.pone.0038528
call_split See protocol

[…] strains in GC, GU, SG, and AG. Comparison was also performed by GC vs GU, GU vs AG, GC vs SG, and AG vs SG. Signal ratios of two hybridized strains were log2 transformed and imported into a web tool ADaCGH, which was used for the analysis of microarray datasets to show gains and losses of genes between the two genomes. The data was centered and segmented in ADaCGH by employing a position-dependen […]

library_books

Parsimonious Higher Order Hidden Markov Models for Improved Array CGH Analysis with Applications to Arabidopsis thaliana

2012
PLoS Comput Biol
PMCID: 3257270
PMID: 22253580
DOI: 10.1371/journal.pcbi.1002286

[…] analyzing Array-CGH data. The standard method for the analysis of the Array-CGH data set measured on a NimbleGen tiling array is the segMNT algorithm . Additionally, all eight methods provided by the ADaCGH webserver including the best performing methods of two in-depth comparison studies , were applied to the Arabidopsis Array-CGH data set. From these eight methods, only ACE , CBS , FHMM , and […]

library_books

SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools a compass in the land of biomarker discovery

2011
J Transl Med
PMCID: 3189883
PMID: 21929757
DOI: 10.1186/1479-5876-9-155

[…] generation sequencing analysis Website: http://www.geospiza.com/Contact/genesiftertrial_ng.shtml License needed:YesName: ADaCGHComment:Web tool for the analysis of aCGH data sets Website: http://adacgh.bioinfo.cnio.es/ License needed:NoName: ArrayStarComment:Gene expression analysis software package that includes visualization tools to help analyze microarray data, including Venn diagrams, a […]

library_books

A survey of analysis software for array comparative genomic hybridisation studies to detect copy number variation

2010
Hum Genomics
PMCID: 3525224
PMID: 20846932
DOI: 10.1186/1479-7364-4-6-421

[…] most suitable, since they do not require software installation and there are no concerns about the hardware. Some of the available tools are analysis of array-based comparative genomic hybridisation (ADaCGH)[] and in silico array-CGH (ISACGH)[] (see Table ). Some of the tools are implemented in MATLAB or an executable file with a very simple interface which guides the user through the analysis (Ta […]

library_books

Cancer gene discovery in mouse and man

2009
Biochim Biophys Acta
PMCID: 2756404
PMID: 19285540
DOI: 10.1016/j.bbcan.2009.03.001

[…] ere the copy number changes significantly , Hidden Markov Models (HMMs) , hierarchical clustering along chromosomes and smoothing methods . There are also a number of web-based applications, such as ADaCGH and CGHweb , for viewing and comparing outputs from multiple algorithms. Further methods have been developed to identify copy number changes specifically in SNP array CGH data, which has incre […]


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ADaCGH institution(s)
Department of Biochemistry, Universidad Autónoma de Madrid, Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (UAM-CSIC), Madrid, Spain

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