IntOGen

Integrative OncoGenomics (IntOGen: http://www.intogen.org), a discovery tool for cancer researchers, is a resource that integrates multidimensional OncoGenomics Data for the identification of genes and groups of genes (biological modules) involved in cancer development.

Reference: Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney S and Lopez-Bigas N. IntOGen: Integration and data-mining of multidimensional oncogenomic data. Nature Methods, 7, 92-93 (2010)

Gitools

Gitools (http://www.gitools.org) is a framework for analysis and visualization of genomic data. Data and results are represented as interactive heatmaps. Gitools allows importing data directly from IntOGen, Biomart, KEGG and Gene Ontology. It performs several analyses like enrichment analysis, correlations, overlaps, identification of driver alterations and combination of experiments.

Reference: Christian Perez-Llamas and Lopez-Bigas N. Gitools: analysis and visualization of genomic data using interactive heat-maps. PLoS ONE 6, e19541 (2011)

Condel

Condel (http://bg.upf.edu/condel) is a method to integrate the output of various methods to identify deleterious non-synonymous variants, which we have shown to perform significantly better that any of the methods alone. Condel outputs a score for each SNVs that can be used as an indicator of the impact of the mutation on the functionality of the mutant protein.

Reference: Abel Gonzalez-Perez and Lopez-Bigas N. Improving the assessment of the outcome of non-synonymous SNVs with a Consensus deleteriousness score (Condel). Am J Hum Genet, 88(4):440-9 (2011).