LocusZoom protocols

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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

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  • person_outline Cristen J. Willer <>

Publication for LocusZoom

LocusZoom in pipelines

 (33)
2017
PMCID: 5226683
PMID: 28076348
DOI: 10.1371/journal.pgen.1006516

[…] haploview: https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview, impute2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html, locuszoom: http://locuszoom.sph.umich.edu/locuszoom/, metasoft: http://genetics.cs.ucla.edu/meta, oragene discover kit ogr-250 by dna genotek: http://www.dnagenotek.com/us/products/ogr250.html, […]

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

[…] association studies (gwas) for maternal and fetal common snps using a linear model implemented in plink software () (–linear, taking into account the effect of the covariates). then, we used the locuszoom (; 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 significance […]

2017
PMCID: 5454371
PMID: 28516910
DOI: 10.1038/ncomms15353

[…] hrs, http://hrsonline.isr.umich.edu/, impute2, https://mathgen.stats.ox.ac.uk/impute/impute_v2.html, metal, http://csg.sph.umich.edu/abecasis/metal/, locuszoom, http://csg.sph.umich.edu/locuszoom/, magenta, https://www.broadinstitute.org/mpg/magenta/, plink, http://pngu.mgh.harvard.edu/~purcell/plink/, r metafor, […]

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. ). statistical analysis for quality control, χ2 test of association, logistic regression for adjustment of p values and multi-dimensional scaling for population […]

2017
PMCID: 5709719
PMID: 28878339
DOI: 10.1038/jhg.2017.82

[…] applied, and snps with more than 1% un-imputed genotype data, an maf less than 1% and an hardy–weinberg equilibrium p-value less than 0.0001 were eliminated. regional association plot was written by locuszoom. linkage disequilibrium maps were written by haploview software using genotype of snps shared among our thai data set, gse17205 (hapmap ceu), gse17206 (hapmap chb+jpt) and gse17207 (hapmap […]


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LocusZoom in publications

 (324)
PMCID: 5948839
PMID: 29751835
DOI: 10.1186/s12881-018-0603-z

[…] were also performed using plink software. genome-wide associations were visualized by a software program (r, version 3.4.0; the r foundation). regional associations were visualized with the locuszoom web tool (http://locuszoom.org/)., the demographic information on the final set of 340 non-hispanic caucasian participants and summary statistics on the csf bace are showed in table . […]

PMCID: 5946407
PMID: 29747637
DOI: 10.1186/s12920-018-0364-8

[…] after anova. genome-wide associations were visualized using a software program (r, version 3.4.0; the r foundation). regional associations were visualized with the locus zoom web tool (http://locuszoom.org/). moreover, a multiple linear regression model was applied using plink to estimate coefficients for testing a possible correlation between brain structure and rs7943454. age, gender, […]

PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z

[…] sex-specific effect estimates were generated using stratified logistic regression models. y chromosome data were analyzed using logistic regression in snptest (fig. ). figures were generated using locuszoom and r 3.3.2 using genabel, qqman, and ggplot–., only newly diagnosed cases from tcga gbm and lgg with no neo-adjuvant treatment or prior cancer were used. demographic characteristics, […]

PMCID: 5940788
PMID: 29739929
DOI: 10.1038/s41467-018-04086-y

[…] p value was lower than 5.0 × 10−8. genome-wide manhattan and q–q plots were generated using the qqman r package (version 0.1.2). regional manhattan plots for the associated loci were generated using locuszoom standalone. the genotype data from the individuals included in the ukbb data set was used to estimate a more accurate ld structure., the genomic inflation factor (λgc) was calculated […]

PMCID: 5934841
PMID: 29724251
DOI: 10.1186/s13075-018-1590-3

[…] based on ld (r2 < 0.3) excluded 39 snps from the list, leaving 9 snps with potential independent signals (additional file : table s3). among them, snp rs13440883 showed the most prominent signal. locuszoom [] was used to plot the regional (± 200 kb) association signal (additional file : figure s2). the association of rs13440883 was detected in both asian and european data, with a slightly […]


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

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