qqman protocols

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qqman specifications


Unique identifier OMICS_12451
Name qqman
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.1.4
Stability Stable
knitr, R(≥3.0.0), calibrate
Source code URL https://cran.r-project.org/src/contrib/qqman_0.1.4.tar.gz
Maintained Yes



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  • person_outline Stephen Turner <>

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Publication for qqman

qqman in pipelines

PMCID: 5443641
PMID: 28560331
DOI: 10.1126/sciadv.1602404

[…] average fst values for nonoverlapping 5-kb windows, and (iii) calculated fst values for individual snps. we built manhattan plots and conducted pca in r version 3.3.0 () with the packages “qqman” and snprelate version 3.3 (), respectively. the pca derived from 11.5 million snps was run both with and without four outlier individuals (two s. melanogaster and two s. pileata; see details […]

PMCID: 5438072
PMID: 27029810
DOI: 10.1038/ncomms11174

[…] (cphm) excluding genotype using the r package survival and then used plink 1.9 (ref. ) to perform a gwas scan at array snps for these residuals. manhattan plots were created in r using the package qqman. for the two clearly associated regions, we then created locus zoom plots using imputed genotypes and the martingale residuals (the discovery phase). the top array snp for mothers and fathers […]

PMCID: 4649671
PMID: 25687228
DOI: 10.1038/srep08517

[…] was performed using program mach v1·0, with genotype data for 286 east-asian samples (chb, 97; chs, 100; jpt, 89) from 1000 genomes project released in june 2011 as reference panel. the r package qqman was utilized to create quantile-quantile (q-q) plot and manhattan plot. haploview software was utilized to analyze and visualize the ld pattern of the interested variants. the in-house […]

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qqman in publications

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

[…] 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, molecular classification and somatic […]

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

[…] associations were considered significant and taken forward for replication if the ukbb discovery 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 […]

PMCID: 5941644
PMID: 29739359
DOI: 10.1186/s12881-018-0587-8

[…] analysis was conducted using eigenstrat [] and individuals falling greater than six standard deviations from the mean of each vector were removed. q-q and manhattan plots were generated using the qqman package [] in r (https://www.r-project.org/)., demographic and clinical characteristics were compared using t-tests for continuous traits and chi-squared tests for dichotomous traits. […]

PMCID: 5921553
PMID: 29703154
DOI: 10.1186/s12864-018-4698-6

[…] in solar eclipse version 7.6.4. bonferonni corrections were used to account for multiple testing in phenotypic and genetic correlations. we used rcircos package and a modified version of the qqman package in r software to make the circos plot and the chromosomic representations. []. finally, we used the ipa system (ingenuity® systems, www.ingenuity.com) to analyze pathways […]

PMCID: 5932955
PMID: 29755503
DOI: 10.3389/fgene.2018.00128

[…] this case was also implemented using the software gemma., we generated manhattan and quantile-quantile (q-q) plots for ew traits using the “gap” (https://cran.r-project.org/web/packages/gap/) and “qqman” (https://cran.r-project.org/web/packages/qqman/) packages within the software r. a genomic inflation factor (λ) was also calculated using the “genabel” package in r (devlin, ) to evaluate […]

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qqman institution(s)
Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA

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