Deciphering Squamous Cell Carcinoma Using Multidimensional Genomic Approaches

Table 3

Software for integrative analysis of Multidimensional omics data.

Program	Application	Website	Reference
Agilent Genomic Workbench 5.0	Genomics	http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnaanalyticssoftware/pages/default.aspx
	Epigenomics		n/a
	Transcriptomics
SIGMA2	Genomics	http://www.flintbox.com/technology.asp?page=3716
	Epigenomics		[85, 86]
	Transcriptomics
Integrative Genomics Viewer	Genomics; Transcriptomics	http://www.broadinstitute.org/igv/	n/a
Nexus Copy Number	Genomics; Transcriptomics	http://www.biodiscovery.com/index/nexus	n/a
CGH Fusion	Genomics; Transcriptomics	http://www.infoquant.com/index/cghfusion	n/a
ISA-CGH	Genomics; Transcriptomics	http://www.isacgh.bioinfo.cipf.es	[87]
VAMP	Genomics	http://www.bioinfo-out.curie.fr/projects/vamp/
	Epigenomics		[88]
	Transcriptomics
Partek Genomics Suite	Genomics	http://www.partek.com/partekgs
	Epigenomics		n/a
	Transcriptomics
	Genomics	http://www.GenomicsPortals.org/
Genomics Portals	Epigenomics		[89]
	Transcriptomics
CHESS	Genomics; Transcriptomics	http://www.biostone.khu.ac.kr/CHESS	[90]
integrOmics	Genomics	http://www.CRAN.R-project.org/
	Epigenomics		[91]
	Transcriptomics
SEURAT	Genomics	http://www.seurat.r-forge.r-project.org/
	Epigenomics		[92]
	Transcriptomics
Genome Studio	Genomics	http://www.illumina.com/software/genomestudio_software.ilmn
	Epigenomics		n/a
	Transcriptomics