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Gene ARMADA specifications

Information


Unique identifier OMICS_01821
Name Gene ARMADA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Affymetrix, Agilent Technologies
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License Academic Free License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for Gene ARMADA

Gene ARMADA citations

 (5)
library_books

Systems biology combining human and animal data miRNA and mRNA data identifies new targets in ureteropelvic junction obstruction

2017
BMC Syst Biol
PMCID: 5333413
PMID: 28249581
DOI: 10.1186/s12918-017-0411-7

[…] For the microarrays statistical analysis the freely available software Gene ARMADA was used []. A background correction was made for all arrays by loess correction and normalization was made by linear lowess followed by quantile normalization. The statistically different […]

library_books

Comparative Meta Analysis of Transcriptomics Data during Cellular Senescence and In Vivo Tissue Ageing

2015
PMCID: 4419258
PMID: 25977747
DOI: 10.1155/2015/732914

[…] d normalization were the first preprocessing steps to homogenize retrieved data and compensate for systematic error measurements among different experimental platforms. These steps were performed by “Gene ARMADA” (Automated Robust Microarray Data Analysis), a MATLAB implemented, microarray, statistical analysis platform, equipped with a graphical user interface (GUI) (http://www.grissom.gr/armada/ […]

library_books

A Comparative Genomic Study in Schizophrenic and in Bipolar Disorder Patients, Based on Microarray Expression Profiling Meta Analysis

2013
Sci World J
PMCID: 3608181
PMID: 23554570
DOI: 10.1155/2013/685917

[…] The raw signal intensity data of each study were imported into the Gene Automated and Robust MicroArray Data Analysis (Gene ARMADA) software tool [] for versatile, microarray data analysis. In order to extract the signal intensities from the raw data, specific steps were followed: background correction was performed w […]

library_books

Performance in Omics Analyses of Blood Samples in Long Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research

2013
Environ Health Perspect
PMCID: 3620742
PMID: 23384616
DOI: 10.1289/ehp.1205657

[…] r’s recommendations. We preprocessed the data with the GenomeStudio (version 2011.1) Methylation module (version 1.9; Illumina) and evaluated them using an adaptation of HumMeth27QCReport (). We used Gene ARMADA () for within- and between-array normalization (linear LOESS and A-quantile, respectively) and imputation of missing values (k nearest neighbors approach).Metabolomics. We analyzed plasma […]

library_books

Application of an Integrative Computational Framework in Trancriptomic Data of Atherosclerotic Mice Suggests Numerous Molecular Players

2012
Adv Bioinformatics
PMCID: 3502768
PMID: 23193398
DOI: 10.1155/2012/453513

[…] ed, biological experts. To overcome this limitation, user friendly software packages for normalization, statistical analysis, and visualization of microarray expression data have been developed, like Gene ARMADA [] and FlexArray []. Regarding pathway analysis, multiple software tools are exploiting ontological vocabularies to target the issue of detecting over-represented terms in microarray datas […]

Citations

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Gene ARMADA institution(s)
Metabolic Engineering and Bioinformatics Group, Institute of Biological Research and Biotechnology, National Hellenic Research Foundation, Athens, Greece

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