OncoPaD specifications

Information


Unique identifier OMICS_13761
Name OncoPaD
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Mutational drivers of one or more tumor types and well-known cancer genes, manually collected driver genes bearing alterations known to influence anti-tumor drug effects (biomarkers maintained in an in-house database), user-defined genes of interest
Output data Reports including all charts and tables, the genomic location of the panel candidates in BED file
Output format PDF
Programming languages Python
Computer skills Basic
Stability Stable
Requirements
Javascript
Maintained Yes

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Documentation


Maintainer


  • person_outline Carlota Rubio-Perez <>

Additional information


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Information


Unique identifier OMICS_13761
Name OncoPaD
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Mutational drivers of one or more tumor types and well-known cancer genes, manually collected driver genes bearing alterations known to influence anti-tumor drug effects (biomarkers maintained in an in-house database), user-defined genes of interest
Output data Reports including all charts and tables, the genomic location of the panel candidates in BED file
Output format PDF
Operating system Unix/Linux
Programming languages Python
Computer skills Medium
Stability Stable
Requirements
Javascript
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Carlota Rubio-Perez <>

Additional information


A registration is needed to access to tools.

Publication for OncoPaD

OncoPaD in publication

PMCID: 5706302
PMID: 29183400
DOI: 10.1186/s13073-017-0493-2

[…] et al. [] compiled a list of known cancer driver genes and calculated the cumulative mutational frequency of those genes in a data set of 28 cancer types. they then designed a web interface called oncopad that could suggest the most relevant set of genes for different cancer types chosen by the user. these genes were further classified into tiers 1, 2 and 3, with tier 1 genes contributing […]


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OncoPaD institution(s)
Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
OncoPaD funding source(s)
This work was partly supported by a Ramón y Cajal contract (RYC-2013-14554), by an FPI fellowship, by the People Programme (Marie Curie Actions) of the Seventh Framework Programme of the European Union (FP7/2007- 2013) under REA grant agreement no. 600388 and by the Agency of Competitiveness for Companies of the Government of Catalonia, ACCIÓ. This work also received funding from the Spanish Ministry of Economy and Competitiveness (grant no. SAF2012-36199), the Marató de TV3 Foundation, and the Spanish National Institute of Bioinformatics (INB).

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