OncoScore specifications

Information


Unique identifier OMICS_16740
Name OncoScore
Interface Web user interface
Restrictions to use None
Input data A list of gene.
Output data The output of the analysis is a score representing the strength of the association of any gene symbol to cancer, based on the literature available at the time of the analysis.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Piazza Rocco

Information


Unique identifier OMICS_16740
Name OncoScore
Software type Package/Module
Interface Command line interface, Web user interface
Restrictions to use None
Output data The output of the analysis is a score representing the strength of the association of any gene symbol to cancer, based on the literature available at the time of the analysis.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.1
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Piazza Rocco

Publication for OncoScore

OncoScore citations

 (2)
library_books

Concomitant BCORL1 and BRAF Mutations in Vemurafenib Resistant Melanoma Cells1

2018
PMCID: 5915992
PMID: 29605720
DOI: 10.1016/j.neo.2018.02.009

[…] a 1071-1077). Glutamine 1076 is very conserved across species (Supplementary Figure S6), and the Q1076H substitution was indicated as possibly damaging by SIFT and PolyPhen-2 algorithms. According to OncoScore , BCORL1 is a cancer-causing gene, with a score of 62.2 (values >21 are considered oncogenic).Figure 2Figure 2In order to verify the biological relevance of these findings, p47BRAFV600E and […]

library_books

Simul seq: combined DNA and RNA sequencing for whole genome and transcriptome profiling

2016
Nat Methods
PMCID: 5734913
PMID: 27723755
DOI: 10.1038/nmeth.4028

[…] Somatic variant analysis was performed using Bina tumor-normal whole-genome calling workflow. Briefly, somatic variants with a Bina ONCOSCORE of greater than or equal to 5 were considered high confidence and reported. To identify somatic variants and generate the ONCOSCORE, Bina integrates JointSNVMix 0.7.5 (), Mutect 2014.3-24-g7 […]

OncoScore institution(s)
University of Milano-Bicocca, Department of Medicine and Surgery, Monza, Italy; Stanford University, Department of Pathology, CA, USA; GalSeq s.r.l., Monza, Italy; University of Milano-Bicocca, Department of Informatics, Milano, Italie; University of New Mexico, Department of Pediatrics, Albuquerque, NM, USA
OncoScore funding source(s)
This work was supported by Associazione Italiana Ricerca sul Cancro 2013 (IG-14249), by Associazione Italiana Ricerca sul Cancro 2015 (IG-17727), by Fondazione Berlucchi (2014) and by European Union’s Horizon 2020 Marie Skłodowska-Curie Innovative Training Networks (ITN-ETN) under grant agreement No.: 675712CGP.

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