LocusZoom protocols

LocusZoom specifications

Information


Unique identifier OMICS_04408
Name LocusZoom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Cristen J. Willer <>

Publication for LocusZoom

LocusZoom IN pipelines

 (22)
2017
PMCID: 5207643
PMID: 28046027
DOI: 10.1371/journal.pone.0168137

[…] generated using r version 3.0.2 software (http://www.r-project.org/), and regional plots with a 1-megabase (mb) window centered at the variant with the peak snp were constructed using the web-based locuszoom tool [23]., in the replication analysis, linear regression analyses of the lipid ratios were performed to confirm the association of the gwas snps in the kdc population, with adjustment […]

2017
PMCID: 5386877
PMID: 28235828
DOI: 10.1534/g3.117.039784

[…] (gwas) for maternal and fetal common snps using a linear model implemented in plink software (purcell et al. 2007) (–linear, taking into account the effect of the covariates). then, we used the locuszoom (pruim et al. 2011; http://locuszoom.sph.umich.edu/locuszoom/) tool to generate regional genomic plots and assess linkage disequilibrium (ld) among associated snps. we use the genome-wide […]

2017
PMCID: 5457519
PMID: 28534485
DOI: 10.1038/ncomms15466

[…] additional covariates, we tested for independence of our 14 associated snps from the two snps (rs3825942 and rs1048661) of the original published locus. regional association plots were created using locuszoom version 1.1 (ref. 70). statistical analysis for quality control, χ2 test of association, logistic regression for adjustment of p values and multi-dimensional scaling for population […]

2016
PMCID: 4698720
DOI: 10.1038/srep18092

[…] of the observed and expected p-values for all eligible snps60. regional plots showing ld and the location of nearby genes were generated for the top ranking snps for each metabolite using locuszoom v1.1, build hg19/1000 genomes mar 2012 eur (http://csg.sph.umich.edu/locuszoom/)61. if more than one significant snp clustered at a locus, the snp with the smallest p-value was reported […]

2016
PMCID: 4698720
DOI: 10.1038/srep18092

[…] plots showing ld and the location of nearby genes were generated for the top ranking snps for each metabolite using locuszoom v1.1, build hg19/1000 genomes mar 2012 eur (http://csg.sph.umich.edu/locuszoom/)61. if more than one significant snp clustered at a locus, the snp with the smallest p-value was reported as the sentinel marker. all analyses were performed using beagle v3.3.154, […]

LocusZoom institution(s)
Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI, USA

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