Table 1 Multiple cancer data type visualization and/or integration resources

Caleydo StratomeX [24]

Tools allowing exploration of relationship among multiple datasets

Multi-omic

Application/Java

Data visualization

Windows Unix/Linux Mac OS

CAS-viewer [25]

Visualization of Cancer Alternatively Splicing (CAS) is a dynamic interface providing an integrated knowledge of alternative mRNA splicing patterns along with multi-cancer omic data from 33 TCGA cancer types

DNA methylation, miRNAs, and SNPs

Web Application/-

Data visualization and basic analysis

Windows Unix/Linux Mac OS

cBio Cancer Genomic Portal [26, 27]

The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets from The Cancer Genome Atlas as well as many carefully curated published data sets

Transcriptomic, DNA methylation, CNVs, SNPs and clinical data

Web Application/Python, Java, Perl, R, MatLab

Data visualization and basic analysis

Windows

Unix/Linux Mac OS

Genboree Workbench [28]

Genboree is a web-based platform for multi-omic research and data analysis using the latest bioinformatics tools.

Transcriptomic and epigenomic data

Web Application/-

Data visualization and basic analysis

Windows Unix/Linux Mac OS

MARIO [29]

MArkov Random fields to Integrate Omics variables (MARIO) is a hierarchical Bayesian model approach for the parallel, integrative analysis of data from several genomic types

Multi-omic and beyond

BUGS software/-

Data integration/analytics

Unix/Linux

mixOmics [30]

mixOmics offers exploration and integration of biological data and allows multivariate statistical approaches to identify similarities between two heterogeneous datasets

Multi-omic and beyond

Bioconductor Package/R

Data integration/analytics

Windows Unix/Linux Mac OS

ModulOmics [31]

ModulOmics identifies cancer driver pathways, or modules, by integrating multiple data types on the basis of DNA and RNA cancer patient data, integrated with PPI networks and known regulatory connections

Multi-omic and beyond

Package/R or Python

Data integration/analytics

Unix/Linux Mac OS

Omics Integrator [32]

Omics Integrator provides integration of proteomic data, gene expression data and/or epigenetic data using a protein–protein interaction network. It is comprised of two modules, Garnet and Forest

Multi-omic and beyond

Package/Python

Data integration/analytics

Unix/Linux

XENA UCSC browser [33]

It offers interactive visualization and exploration of TCGA genomic, phenotypic, and clinical data, as produced by the Cancer Genome Atlas Research Network

Multi-omic

Web client

Data visualization

Windows Unix/Linux Mac OS