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Oncodrive-fm specifications

Information


Unique identifier OMICS_00157
Name Oncodrive-fm
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
the Statistics::Descriptive, R
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Abel González-Pérez

Publication for Oncodrive-fm

Oncodrive-fm citations

 (8)
library_books

Aggressive natural killer cell leukemia mutational landscape and drug profiling highlight JAK STAT signaling as therapeutic target

2018
Nat Commun
PMCID: 5908809
PMID: 29674644
DOI: 10.1038/s41467-018-03987-2

[…] n the analysis, conversion of EnsEMBL to UCSC chromosome nomenclature was done using the function mapSeqlevels from the package GenomeInfoDb. Potential driver genes were identified using MutSigCV and Oncodrive-fm. MutSigCV was executed using the default mutation rate covariate after fixing its gene names to current nomenclature with maftools, a hg38-compatible coverage file generated with the CovG […]

library_books

Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse associated genes

2016
Oncotarget
PMCID: 5325426
PMID: 27590521
DOI: 10.18632/oncotarget.11773

[…] tered based on sequence coverage, quality scores and germline variants, and annotated against the Ensembl database as described previously []. Putative driver genes were identified using MutSigCV [], Oncodrive-fm [] and OncodriveCLUST [] as described previously [], except that OncodriveCLUST version 0.4.1 was used. For this analysis, the 172 patients in the diagnostic cohort were divided into five […]

library_books

Inactivation of TGFβ receptors in stem cells drives cutaneous squamous cell carcinoma

2016
Nat Commun
PMCID: 5007296
PMID: 27558455
DOI: 10.1038/ncomms12493

[…] on the significance (P-value) of the FM bias (that is, the bias towards the accumulation of mutations with high functional impact). The significantly mutated signalling pathways (based on the IntOGen Oncodrive-fm functional impact bias, FM bias P<0.05) were further selected (). MutsigCV was also used to detect significant genes with point mutations above the background mutation rate. […]

library_books

TCF12 is mutated in anaplastic oligodendroglioma

2015
Nat Commun
PMCID: 4490400
PMID: 26068201
DOI: 10.1038/ncomms8207

[…] rporated mutation data from multiple tumour types using Oncodrive-fm implemented within the IntOGen-mutations platform (). The most recurrently mutated genes according to MutSig were also detected by Oncodrive-fm as significantly mutated (Q-value<0.05). Oncodrive-fm also identified a number of other important mutated genes (that is, displaying high FM bias) including SETD2, NOTCH2, RBPJ, ARID1A, A […]

library_books

Whole exome sequencing reveals the mutational spectrum of testicular germ cell tumours

2015
Nat Commun
PMCID: 4338546
PMID: 25609015
DOI: 10.1038/ncomms6973

[…] l samples. MutSigCV was run using the standard genomic covariates of (i) global gene expression data, (ii) DNA replication time and (iii) HiC statistic of open versus closed chromatin states. We used Oncodrive-fm as implemented within the IntOGen-mutations platform, using data mutation data from multiple tumour studies (http://bg.upf.edu/group/projects/oncodrive-fm.php; http://www.intogen.org/anal […]

library_books

The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing

2014
Hum Mutat
PMCID: 4309499
PMID: 25355294
DOI: 10.1002/humu.22719

[…] L patients. In addition to KRAS and NOTCH1, we identified KMT2D, KIF1B (MIM# 605995) and ME1 (MIM# 154250) as novel putative driver genes using three complementary tools (MutSigCV, Lawrence et al. () Oncodrive-fm, Gonzalez-Perez, Lopez-Bigas () and OncodriveCLUST, Tamborero et al. ()). To find subtype-specific patterns, we analyzed the T-ALL samples and the largest BCP-ALL subtypes (HeH, t(12;21), […]

Citations

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Oncodrive-fm 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
Oncodrive-fm funding source(s)
This work was supported by the Spanish Ministry of Science and Technology [SAF2009-06954] and the Spanish National Institute of Bioinformatics.

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