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qqman specifications

Information


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
Requirements
knitr, R(≥3.0.0), calibrate
Source code URL https://cran.r-project.org/src/contrib/qqman_0.1.4.tar.gz
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Stephen Turner

Additional information


https://cran.r-project.org/web/packages/qqman/qqman.pdf

Publication for qqman

qqman citations

 (130)
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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

2018
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–. […]

call_split

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

2018
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 […]

library_books

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

2018
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 […]

call_split

Familial resemblances in human whole blood transcriptome

2018
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 […]

library_books

Genome Wide Association Analysis of Age Dependent Egg Weights in Chickens

2018
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 […]

library_books

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

2018
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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