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Citations per year

Number of citations per year for the bioinformatics software tool GAIA

Tool usage distribution map

This map represents all the scientific publications referring to GAIA per scientific context
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GAIA specifications


Unique identifier OMICS_19281
Alternative name Genomic Analysis of Important Alterations
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 2.24.0
Stability Stable
Maintained Yes




No version available



  • person_outline Michele Ceccarelli
  • person_outline Luigi Cerulo

Additional information

Publications for Genomic Analysis of Important Alterations

GAIA citations


Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas

PMCID: 5908308
PMID: 29682207
DOI: 10.18632/oncotarget.24907

[…] lysis, including gene coding, UTR, and promoter region and labelled each with HGVS protein ID where available. Recurrent SCNA in the GISTIC 2.0 SCNA data was calculated separately for each race using GAIA [] by first building a copy number variant (CNV) matrix of regions used by GISTIC 2.0, less known common CNV (available at Recurrent CNV […]


TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] xHeatmap _ 1.10.2 60 [43] dnet _ 1.0.9 61 [44] supraHex _ 1.10.0 62 [45] hexbin _ 1.27.1 63 [46] igraph _ 1.0.1 64 [47] circlize _ 0.3.7 65 [48] pbapply _ 1.2–1 66 [49] gplots _ 3.0.1 67 [50] gaia _ 2.16.0 68 [51] readr _ 0.2.2 69 [52] downloader _ 0.4 70 [53] TCGAbiolinks _ 2.1.0 71 72 loaded via a namespace (and not attached): 73 [1] SparseM _ 1.7 ggthemes _ 3.2.0 74 [3] prab […]


Comparative Analysis of Methods for Identifying Recurrent Copy Number Alterations in Cancer

PLoS One
PMCID: 3527554
PMID: 23285074
DOI: 10.1371/journal.pone.0052516

[…] In contrast to other existing methods , , , GAIA (Genomic Analysis of Important Alterations) incorporates within-sample homogeneity into the “peel-off” procedure under its statistical hypothesis framework: first, individual markers are randomly […]

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GAIA institution(s)
Department of Science and Technology, University of Sannio, Benevento, Italy; BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Ariano Irpino (AV) Italy; Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
GAIA funding source(s)
Supported by a research project funded by MiUR (Ministero dell’Università e della Ricerca) under grant FIRB2012-RBFR12QW4I.

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