eSNV-detect statistics

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eSNV-detect specifications


Unique identifier OMICS_06134
Name eSNV-detect
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for eSNV-detect

eSNV-detect in publications

PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] in expression levels; and 4) rna editing sites being confused as dna mutations., currently there are at least variant callers that accept rna-seq data: radia, seurat, vardict, varscan2, snpir, and esnv-detect , , , , , . radia and seurat do not analyze rna-seq data alone, but integrate rna-seq with matched tumor-normal dna from the same patient to improve the accuracy. radia showed that real […]

PMCID: 5681780
PMID: 29126398
DOI: 10.1186/s12864-017-4261-x

[…] expression of two alleles, we first need to identify genes with heterozygous snps. there are software programs that can call snps from bulk rna-seq datasets, such as gatk [], samtools [], and esnv-detect []. however, they usually do not work as well on rna-seq data as they do on genomic sequencing data, because the assumption of a 1:1 ratio of the two parental alleles are often violated […]

PMCID: 3815156
PMID: 24223926
DOI: 10.1371/journal.pone.0079298

[…] genotype calling algorithms for snvs were designed for germline dna and not for rna. hence, the false detection rates to call an snv are high in rna-seq data from tumors. we have developed an esnv-detect (expressed single nucleotide variant detection) workflow with parallel alignment strategies (bowtie and bwa). the advantage of using two aligners in esnv-detect is that we take […]

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eSNV-detect institution(s)
Division of Biomedical Statistics and Informatics, Mayo Clinic, Chinahester, MN, USA; Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Chinahester, MN, USA,Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Chinahester, MN, USA; Fluidigm Corporation, South San Francisco, CA, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA

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