SNPEVG statistics

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Associated diseases

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SNPEVG specifications

Information


Unique identifier OMICS_04391
Name SNPEVG
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SNPEVG

SNPEVG in publications

 (11)
PMCID: 5829525
PMID: 28672053
DOI: 10.1111/bjd.15787

[…] ma, u.s.a.) for generating manhattan plots, locuszoom (department of biostatistics, center for statistical genetics, university of michigan, ann abor, mi, u.s.a.) for regional visualization and snpevg (university of minnesota, st paul, mn, u.s.a.) for a corresponding q–q plot to evaluate differences between cases and controls caused by potential confounders (e.g. different genotyping […]

PMCID: 5519714
PMID: 28729714
DOI: 10.1038/s41598-017-06153-8

[…] the 38,765 genotype data after filtering snps with minor allele frequency less than 0.05. manhattan plots were obtained from genome-wide p using a graphical tool for snp effect viewing and graphing (snpevg)., , electronic supplementary material , supplementary information accompanies this paper at doi:10.1038/s41598-017-06153-8 , publisher's note: springer nature remains neutral […]

PMCID: 5326497
PMID: 28235410
DOI: 10.1186/s12711-017-0299-0

[…] the threshold p value for declaring genome-wide significance was 0.05/(2 × 45,611) = 5.48 × 10−7. the manhattan plots of the p values for all snps associated with tew and tep were plotted using snpevg1 version 2.1 []. gene locations and information were mined from the ensembl chicken genome galgal 3 []., gwas were also carried out with mixed-model statistical packages, including gapit […]

PMCID: 4855826
PMID: 27124316
DOI: 10.1167/iovs.16-19332

[…] to be significant., other gwas-related software used in our study were: snpnexus for snp functional annotation, haploview for generating manhattan plots and linkage disequilibrium (ld) blocks, and snpevg for generating corresponding quantile-quantile (q-q) plot to evaluate differences between cases and controls caused by potential confounders (different genotyping laboratories, different dna […]

PMCID: 4784999
PMID: 27162493
DOI: 10.1270/jsbbs.66.213

[…] (q + k model). a marker-trait association (mta) was considered when the p-value was significant at 0.01 [−log10(0.01) = 2]. manhattan plots were generated based on association mapping results with snpevg ()., sequences from the ril mapping population and core collection were collected in seven 48-plex flow cells. on average, 184,312,348 sequence reads corresponding to 18,615 mb were obtained […]


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SNPEVG institution(s)
Department of Animal Science, University of Minnesota, St Paul, MN, USA

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