Oncotator protocols

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description
Oncotator computational protocol

Oncotator specifications

Information


Unique identifier OMICS_00178
Name Oncotator
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

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Maintainer


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Information


Unique identifier OMICS_00178
Name Oncotator
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages Python
Computer skills Basic
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publication for Oncotator

Oncotator IN pipelines

 (6)
2018
PMCID: 5820260
PMID: 29463849
DOI: 10.1038/s41598-018-20321-4

[…] that all tcga data are now available without restrictions on their use in publications or presentations. single nucleotide variants (snv) for these kirc samples were subsequently annotated by oncotator36 in ucsc cancer browser (ucsc xena now). after removing hyper mutated samples, we transformed them to a 0/1 matrix (patient x mutation gene) and filtered low mutation frequency (<3) […]

2017
PMCID: 5688099
PMID: 29142225
DOI: 10.1038/s41467-017-01730-x

[…] status of the snps. the wes samples were hierarchically clustered by the “dendextend” package in r33., to identify significantly mutated genes, somatic mutations were annotated using oncotator34. mutsigcv (v1.4)19 was applied to identify significantly mutated genes with default covariate tables. genes with q (fdr) < 0.1 were considered to be significantly mutated. we performed […]

2016
PMCID: 4762882
PMID: 26892726
DOI: 10.1038/ncomms10536

[…] supplementary fig. 2; supplementary table 1)., to assess the functional consequences of the variants, the sets of high-confidence unique snvs and indels were annotated using the sgadviser17 and oncotator18 program suites. they were further characterized based on overlaps with encode annotated genomic regions. as expected, most mutations fell within intergenic or intronic regions, […]

2016
PMCID: 5013668
PMID: 27576846
DOI: 10.1038/ncomms12609

[…] and pindel23 were used for the detection of single nucleotide variants and indels with the re-aligned binary sequence alignment/map (bam) files24. the resulting mutation calls were annotated by oncotator11. silent or non-coding mutations were excluded from the analysis along with the known germline tp53 p72r polymorphism. given the difficulties associated with variant calling when using […]

2015
PMCID: 4552571
PMID: 26192918
DOI: 10.1038/ng.3343

[…] http://www.ncbi.nlm.nih.gov/ccds/; broad institute picard sequencing pipeline, http://broadinstitute.github.io/picard/; broad institute firehose pipeline, http://www.broadinstitute.org/cancer/cga; oncotator, […]

Oncotator institution(s)
Cancer Program, Broad Institute, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA

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