QxPak protocols

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QxPak specifications

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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 in pipeline

2012
PMCID: 3432624
PMID: 22607048
DOI: 10.1186/1471-2156-13-41

[…] the kth animal was homozygous for each allele or 0 if the animal was heterozygous; g represented the additive effect of the snp or haplotype., all the statistical analyses were performed using the qxpak v.5.1 software []., a total of 8,417 snps evenly spaced were used for the analyses. the mean distance between snps ranged from 0.18 cm in ssc11 to 0.33 cm in ssc6 (table ). the qtl scan […]

QxPak in publications

 (32)
PMCID: 5844516
PMID: 29522525
DOI: 10.1371/journal.pone.0190184

[…] 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 []., gene content of the qtl regions were determined using biomart tool from the porcine ensembl database, sscrofa11.1. in order to identify potential candidate genes the function […]

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

[…] program., 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 5.0:1\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \ […]

PMCID: 5396199
PMID: 28422154
DOI: 10.1038/srep46539

[…] 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 […]

PMCID: 4989154
PMID: 27666082
DOI: 10.1038/srep31803

[…] tested by using a linear model with r programme., 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 […]

PMCID: 5205596
PMID: 27221246
DOI: 10.5713/ajas.16.0170

[…] 0.81 to 0.96 []., 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 […]

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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