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GenABEL specifications

Information


Unique identifier OMICS_00234
Name GenABEL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained No

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Publication for GenABEL

GenABEL citations

 (471)
library_books

Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

2018
Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] lation-based studies. In samples with related individuals association testing accounting for family structure was conducted using the –fastAssoc option in MERLIN or the –mmscore option implemented in GenABEL. Before meta-analysis, we removed variants with MAF < 0.01, and with imputation quality scores less than 0.3.Ancestry specific meta-analyses (European-specific and Asian-specific) and joint me […]

call_split

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

[…] ates 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–. […]

call_split

Association of Raynaud’s phenomenon with a polymorphism in the NOS1 gene

2018
PLoS One
PMCID: 5919461
PMID: 29698501
DOI: 10.1371/journal.pone.0196279
call_split See protocol

[…] Statistical analysis was performed using R statistical software with the package GenABEL []. We used linear regression model to analyse association between RP and the SNPs accounting for age, sex and the kinship shared by twins in a pair. The p-values were obtained through experim […]

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

[…] ttps://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 extent of false positive signals.We performed a series of linkage disequilibrium (LD) analyses to characterize causative SNPs within strong LD regions […]

library_books

Canine NAPEPLD associated models of human myelin disorders

2018
Sci Rep
PMCID: 5895582
PMID: 29643404
DOI: 10.1038/s41598-018-23938-7

[…] wide association study (GWAS). Fourteen LEMP-affected dogs and 186 controls (i. e. dogs eight years and older that showed no signs of neurological disease) were analyzed with the mixed model from the GenABEL library and the hglm package in the R environment that corrects for the population stratification. Multidimensional scaling analysis was carried with the GenABEL. We used 173k SNP data of addi […]

library_books

Genome Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

2018
Front Genet
PMCID: 5902979
PMID: 29692799
DOI: 10.3389/fgene.2018.00118

[…] If the LD estimate was r2 > 0.05, one of the pairs of SNPs was removed (). The independent SNPs retained by the LD criteria were then used in the MDS analysis, and the results were plotted using the GenABEL package in R v3.2.2 ().We performed genome-wide association studies within five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) u […]

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GenABEL institution(s)
Department of Epidemiology and Biostatistics, Erasmus MC Rotterdam, Postbus, Netherlands

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