GenABEL pipeline

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 Yes

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Publication for GenABEL

GenABEL citations

 (5)
2018
PMCID: 5891602

[…] calculated in terms of overall fst among the seed quality subclusters using the software genepop version 4.2.2 (rousset, 2008). calculation of genome-wide associations was done with the r package genabel (aulchenko et al., 2007) applying a mixed model approximation including the first four principal coordinates as covariates to correct for population stratification. as shown by price et al. […]

2018
PMCID: 5879874

[…] number of tests performed, significance levels were defined at adjusted alpha 10%. genomic inflation factors (gif) were estimated for the two pqtl analyses using estlambda function available in the genabel r package [21]. pairwise linkage disequilibrium (ld) was calculated with ldlink, a web-based application using 1000 genome phase 3 data [22]., association between circulating angptl3 […]

2016
PMCID: 4820539

[…] a full list of funding information and acknowledgements by study can be found in the supplementary note 2., urls, quickest: http://toby.freeshell.org/software/quicktest.shtml, probabel: http://www.genabel.org/packages/probabel, mixable: http://www.genabel.org/packages/mixabel, metal: www.sph.umich.edu/csg/abecasis/metal/, scan: http://www.scandb.org/newinterface/about.html, genecards: […]

2015
PMCID: 4523021

[…] northern italy, central italy, southern italy and islands)., a neighbor-network graph based on between-breeds fst distances was obtained with the software splitstree ver. 4.10 [26]. the r package genabel ver. 1.7-6 [20] was used to build a multi-dimensional scaling (mds) plot, based on a matrix of (1-pairwise genomic kinship) distances between individuals. admixture ver. 1.22 [27] software […]

2015
PMCID: 4287344

[…] individuals with exome sequencing data, 921 had eligible nmr metabolite measurements. single variant analyses were performed using and additive model as implemented in the “mmscore” function in genabel v.1.7–4, adjusting for relatedness., the study protocol was approved by the medical ethics board of the erasmus mc rotterdam, the netherlands. the study included only adults and written […]

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

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