GenABEL protocols

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description
GenABEL computational protocol

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 IN pipelines

 (5)
2018
PMCID: 5879874
PMID: 29619113
DOI: 10.1186/s12263-018-0597-3

[…] 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 […]

2018
PMCID: 5882890
PMID: 29615742
DOI: 10.1038/s41598-018-23860-y

[…] for the gwas, each pea-signal was adjusted for significant covariates from the combined models and rank-transformed to normality by using the ‘rntransform’ function from the r-package genabel(v1.8.0)51. the nsphs includes related individuals and special care has to be taken to avoid relational biases. therefore, all genetic association calculations were carried out as described […]

2016
PMCID: 4820539
PMID: 27020472
DOI: 10.1038/ncomms11008

[…] 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: […]

2013
PMCID: 3658165
PMID: 23535824
DOI: 10.1093/hmg/ddt086

[…] alone, without implementing a two panel imputation., association tests were performed on genotypes in the mach dosage format (0–2) converted from the impute genotype posterior probabilities using genabel (23), and haplotype analyses were performed on ‘best guess’ genotypes converted using gengen; calls are generated only, if the posterior probability is higher than 0.9, unless otherwise […]

2011
PMCID: 3482684
PMID: 21876539
DOI: 10.1038/mp.2011.101

[…] imputed and genotyped snps. for each gwas, the association analysis was performed using linear regression analysis by regressing coffee categories63 on age, sex and snp allele dosage in probabel64 (genabel.org, novosibirsk, russia), snptest65 (jonathan marchini, oxford, uk) or quicktest (toby johnson, lausanne, switzerland) (http://toby.freeshell.org/software/quicktest.shtml) (supplementary […]

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

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