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 <>

LocusZoom article

LocusZoom citations

 (7)
2017
PMCID: 5709719

[…] 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.19 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 […]

2017
PMCID: 5207643

[…] 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 […]

2016
PMCID: 5072673

[…] gwama, http://www.well.ox.ac.uk/gwama/, impute2, http://mathgen.stats.ox.ac.uk/impute/impute_v2.html, snptest, https://mathgen.stats.ox.ac.uk/genetics_software/snptest/old/snptest_v2.1.1.html, locuszoom, http://csg.sph.umich.edu/locuszoom/, r, http://www.r-project.org/, 1000 genomes project, http://www.1000genomes.org/, ensemble variant effect predictor: […]

2016
PMCID: 4731307

[…] and http://genome.ucsc.edu/encode/, genevar, http://www.sanger.ac.uk/resources/software/genevar/, gtex, http://www.gtexportal.org/home/, impute, http://mathgen.stats.ox.ac.uk/impute/impute.html, locuszoom, (http://csg.sph.umich.edu/locuszoom/), mach, http://csg.sph.umich.edu/abecasis/mach/download/, metal, http://csg.sph.umich.edu/abecasis/metal/index.html, neighborhood, […]

2015
PMCID: 4595747

[…] the linkage disequilibrium blocks. linkage disequilibrium structures and haplotype block plots were generated with haploview (v4.2)52. the four significant regions were plotted using the online tool locuszoom54., to explore the regulatory properties of the association signals, we used chromatin state segmentation in lcl data generated by the encode project19. haploreg was used to examine whether […]

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

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