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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 citations

 (11)
library_books

A genome‐wide association study suggests that MAPK14 is associated with diabetic foot ulcers†

2017
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 […]

library_books

Maize (Zea mays L.) genome size indicated by 180 bp knob abundance is associated with flowering time

2017
Sci Rep
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 […]

library_books

TCF21 is related to testis growth and development in broiler chickens

2017
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 […]

library_books

A Genome Wide Association Study Provides New Evidence That CACNA1C Gene is Associated With Diabetic Cataract

2016
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 […]

library_books

Characterization of a mini core collection of Japanese wheat varieties using single nucleotide polymorphisms generated by genotyping by sequencing

2016
Breed Sci
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 […]

library_books

A Genome wide Association Study Provides Evidence of Sex specific Involvement of Chr1p35.1 (ZSCAN20 TLR12P) and Chr8p23.1 (HMGB1P46) With Diabetic Neuropathic Pain

2015
PMCID: 4634194
PMID: 26629533
DOI: 10.1016/j.ebiom.2015.08.001

[…] and the impact of these potential confounders (different genotyping machines, different genotyping chips, different dna extraction methods, etc) between cases and controls, was visualised by snpevg (). the whole workflow is summarised in . narrow-sense heritabilities of the overall dataset and sex-specific dataset were performed by restricted maximum likelihood analysis using […]


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

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