Oncofuse specifications

Information


Unique identifier OMICS_01406
Name Oncofuse
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A list of genomic positions of breakpoints in a pair of fusion partner genes.
Input format TSV
Output format TSV
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.1.1
Stability Stable
Requirements
JRE
Maintained Yes

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Documentation


Maintainer


  • person_outline Francisco J. Novo <>

Information


Unique identifier OMICS_01406
Name Oncofuse
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Francisco J. Novo <>

Publications for Oncofuse

Oncofuse in publications

 (7)
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] using tophat-fusion and the associated downstream filtering pipeline (tophat-fusion post). alternatively with less stringent quality filters, but with calculation of oncogenic potential, we used oncofuse with two complementary filters: passenger probability <0.001, driver probability >0.999 and minimum support reads >10, as well as passenger probability <0.01, driver probability […]

PMCID: 5913625
PMID: 29360925
DOI: 10.1093/annonc/mdy025

[…] with both ends of the translocation only in lnm (figure a inset), a characteristic often seen around res [, ]. the fusion transcript is in-frame and joins esr1 exons 1–6 with dab2 exons 3–15. oncofuse is a naive bayesian classifier built to predict the oncogenic potential of fusion genes [] and this showed the esr1–dab2 fusion to have a score of 0.99 (p < 0.0001). notably, the location […]

PMCID: 5711926
PMID: 29214215
DOI: 10.1038/s41523-017-0048-0

[…] defuse and chimerascan were used to identify mate-pairs supporting novel chimeric transcripts as previously described (). candidates that resulted in open reading frames were annotated using oncofuse. nominated in-frame fusion gene candidates, candidates identified by both defuse and chimerascan, as well as those with known associated functions, and those that harbored intact functional […]

PMCID: 5610242
PMID: 28939823
DOI: 10.1038/s41467-017-00888-8

[…] counts of genes and exons, and cufflinks was used to estimate gene expression (fpkm). genetic variants were called using gatk unified genotyper. fusions were detected using star and filtered using oncofuse. quality of raw and aligned reads was assessed using fastqc and qualimap., fpkm values of six technical samples (pcdna3-hey + dmso, rab25-hey + dmso, rab25-hey + rfp14, each from individual […]

PMCID: 5663522
PMID: 29137350
DOI: 10.18632/oncotarget.19848

[…] ( http://ccb.jhu.edu/software/tophat/fusion_index.shtml). the fusion minimum distance was set to 100000000 and anchor length to 13. tophat-fusion-post results were further filtered using oncofuse (www.unav.es/genetica/oncofuse.html). fusion events were filtered out if a fusion event was reported in a normal pancreatic duct sample, if the fusion event included a gene and partnered […]


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Oncofuse institution(s)
LABS, Persistent Systems, Pingala-Aryabhata, Pune, India; University of Michigan, Ann Arbor, MI , USA

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