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

From: Bringing radiomics into a multi-omics framework for a comprehensive genotype–phenotype characterization of oncological diseases

Name Description Data type Software type/Programming language Key task Operating system Latest update
Caleydo StratomeX [24] Tools allowing exploration of relationship among multiple datasets Multi-omic Application/Java Data visualization Windows Unix/Linux Mac OS 2018
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 2018
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
2018
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 2014
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 2017
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 2018
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 2018
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 2018
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 2017