VarWalker statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VarWalker
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Tool usage distribution map

This map represents all the scientific publications referring to VarWalker per scientific context
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VarWalker specifications

Information


Unique identifier OMICS_12293
Name VarWalker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
Computer skills Advanced
Version 1.0
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Zhongming Zhao

Publication for VarWalker

VarWalker citations

 (4)
library_books

Driver pattern identification over the gene co expression of drug response in ovarian cancer by integrating high throughput genomics data

2017
Sci Rep
PMCID: 5700962
PMID: 29170526
DOI: 10.1038/s41598-017-16286-5

[…] e they are long. In order to filter those long but non-qualified genes (genes which have mutations only because they are long yet they are not driver mutations) we adopted the filtering strategies of VarWalker and computed a probability weight vector (PWV) by formulating a generalized additive model and estimated a relative mutation rate for each gene. The vector of X represents the gene length of […]

library_books

HABP2 p.G534E variant in patients with family history of thyroid and breast cancer

2017
Oncotarget
PMCID: 5522276
PMID: 28402931
DOI: 10.18632/oncotarget.16639

[…] ing additional patient cases and larger PPI network, we could use additional tools that combine mutation data (such as HotNet []) or arbitrary omics data (e.g., KeyPathwayMiner [], NBS [], MUFFIN [], VarWalker []) with signaling networks.In conclusion, no co-segregation of the HABP2 p.G534E was found in three families with NMTC and breast cancer. The variant is not significantly associated with PT […]

library_books

The use of gene interaction networks to improve the identification of cancer driver genes

2017
PeerJ
PMCID: 5274523
PMID: 28149674
DOI: 10.7717/peerj.2568

[…] ey were both developed using the R environment, which provides powerful data analysis and graphical features. DriverNet met the standards set by Bioconductor (). We combined graphs from DriverNet (), VarWalker (), and DawnRank () for our analyses. […]

library_books

LNDriver: identifying driver genes by integrating mutation and expression data based on gene gene interaction network

2016
BMC Bioinformatics
PMCID: 5259866
PMID: 28155630
DOI: 10.1186/s12859-016-1332-y

[…] work- and pathway-based approaches have become one of the most promising methods to prioritize driver mutations and significantly mutated genes due to their abilities to model gene-gene interactions. VarWalker is a network-assisted method to prioritize potential driver genes []. Another method, DawnRank prioritizes altered genes on a single patient level using PageRank algorithm []. DriverNet is a […]


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VarWalker institution(s)
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
VarWalker funding source(s)
This work was partially supported by National Institutes of Health grants (R01LM011177, R03CA167695, P30CA68485, and P50CA095103), the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation, and Ingram Professorship Funds.

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