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Oncodrive-fm

An approach to uncover driver genes or gene modules. It computes a metric of functional impact using three well-known methods (SIFT, PolyPhen2 and MutationAssessor) and assesses how the functional impact of variants found in a gene across several tumor samples deviates from a null distribution. It is thus based on the assumption that any bias towards the accumulation of variants with high functional impact is an indication of positive selection and can thus be used to detect candidate driver genes or gene modules.

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Oncodrive-fm classification

Oncodrive-fm specifications

Software type:
Application/Script
Restrictions to use:
None
Programming languages:
Perl
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Requirements:
the Statistics::Descriptive, R

Oncodrive-fm distribution

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No versioning.

Oncodrive-fm support

Documentation

Maintainer

  • Abel González-Pérez <>

Credits

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Publications

Institution(s)

Research Programme on Biomedical Informatics, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona,Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain

Funding source(s)

This work was supported by the Spanish Ministry of Science and Technology [SAF2009-06954] and the Spanish National Institute of Bioinformatics.

Link to literature

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