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Number of citations per year for the bioinformatics software tool QxPak
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Protocols

QxPak specifications

Information


Unique identifier OMICS_24671
Name QxPak
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Fortran
Computer skills Advanced
Maintained No

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Publication for QxPak

QxPak citations

 (39)
library_books

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

2018
PLoS One
PMCID: 5844516
PMID: 29522525
DOI: 10.1371/journal.pone.0190184

[…] ied in the merged dataset analysis were used for haplotype association. Haplotypes were built using Phase v2.1 [] and association analyses were conducted following the previously described model with Qxpak 5.0 software []. […]

library_books

Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions

2018
Sci Rep
PMCID: 5794915
PMID: 29391556
DOI: 10.1038/s41598-018-20473-3

[…] In order to detect SNPs associated with gene expression levels, eGWAS was performed using as phenotype the expression values of 43 genes in adipose tissue. A mixed model (1) was employed in Qxpak 5.0:1Yijk=Sexi+Batchj+λlal+uk+eijkl,in which Yijk was the kth individual expression record of each one of the 43 analyzed genes, sex (two levels) and batch (corresponding to the slaughterhouse g […]

call_split

Integration of liver gene co expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs

2017
Sci Rep
PMCID: 5396199
PMID: 28422154
DOI: 10.1038/srep46539
call_split See protocol

[…] ession-associated SNPs (eSNPs), GWAS was performed using as phenotype the expression pattern of 43 genes in liver tissue. A mixed model accounting for additive effects (see below) was performed using Qxpak 5.0: in which yijkl is the kth individual gene expression, sex (two levels) and batch (five levels) are fixed effects, λk is a −1, 0, +1 indicator variable depending on the kth individual gen […]

library_books

Expression based GWAS identifies variants, gene interactions and key regulators affecting intramuscular fatty acid content and composition in porcine meat

2016
Sci Rep
PMCID: 4989154
PMID: 27666082
DOI: 10.1038/srep31803

[…] An eGWAS was also performed using the genotypes of BC1_LD animals and the expression values from muscle. A mixed model was employed implemented on Qxpak 5.0: in which yijkl was the kth individual record, sex (two levels) and batch (five levels) were fixed effects, λk was a −1, 0, +1 indicator variable depending on the kth individual genotype […]

call_split

A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in South Korean native cattle, Hanwoo

2016
Asian-Australas J Anim Sci
PMCID: 5205596
PMID: 27221246
DOI: 10.5713/ajas.16.0170
call_split See protocol

[…] A mixed-inheritance animal model was used to detect SNP with additive or dominance effects for growth and carcass quality of Hanwoo. The ‘snp_a’, ‘snp_d’, and ‘snp_ad’ options of Qxpak software (Barcelona, Spain) were applied for each SNP. For each trait, appropriate fixed factors or covariates were fitted in the models (p<0.05) using a general linear model procedure in SAS (S […]

call_split

Genomic structure and marker derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle

2016
BMC Genomics
PMCID: 4791965
PMID: 26979536
DOI: 10.1186/s12864-016-2535-3
call_split See protocol

[…] of genotypes for the k-th SNP across all animals. sjk is a vector that represents the additive effect of the k-th SNP on the j-th trait and E represents the vector of residual effects, E ~ N(0, σe2). QXPAK5 was run for the eight phenotypes using the TagSNP set. The p-values and additive genetic values for each SNP were obtained for each phenotype and used to construct the AWM matrix. The FDR (fals […]


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QxPak institution(s)
Institut Catala de Reçerca i Estudis Avançats, Barcelona, Spain; Departament de Ciencia Animal i del Aliments, Facultat de Veterinaria, Universitat Autonoma de Barcelona, Bellaterra, Spain; Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
QxPak funding source(s)
Supported by startup grant from the Catalan Institute for Research and Advanced Studies and from Universitat Autònoma de Barcelona and Armand Sanchez.

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