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 |
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 |