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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




No version available



  • person_outline Stephen Turner

Additional information


Publication for qqman

qqman citations


Sex specific glioma genome wide association study identifies new risk locus at 3p21.31 in females, and finds sex differences in risk at 8q24.21

Sci Rep
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z
call_split See protocol

[…] 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–. […]


Genome wide association studies for diabetic macular edema and proliferative diabetic retinopathy

BMC Med Genet
PMCID: 5941644
PMID: 29739359
DOI: 10.1186/s12881-018-0587-8
call_split See protocol

[…] nts 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. Association […]


Genome wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure

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

[…] ation. 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 was us […]


Familial resemblances in human whole blood transcriptome

BMC Genomics
PMCID: 5921553
PMID: 29703154
DOI: 10.1186/s12864-018-4698-6
call_split See protocol

[…] analysis 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 overrepresented […]


Genome Wide Association Analysis of Age Dependent Egg Weights in Chickens

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

[…] 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 the e […]


MEST mediates the impact of prenatal bisphenol A exposure on long term body weight development

Clin Epigenetics
PMCID: 5910578
PMID: 29721103
DOI: 10.1186/s13148-018-0478-z

[…] t, the chi-squared test was performed. LINA study data were evaluated by STATISTICA for Windows, Version 12 (Statsoft Inc., USA). 450 k data were analyzed and processed using the R packages minfi and qqman (R version 3.3.1, R Foundation for Statistical Computing).BPA concentrations and DNA methylation levels were log transformed for further statistical analyses. To assess longitudinal associations […]


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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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