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EPACTS specifications

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Unique identifier OMICS_07453
Name EPACTS
Alternative name Efficient and Parallelizable Association Container Toolbox
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.2.6
Stability Stable
Maintained Yes

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https://github.com/statgen/EPACTS

EPACTS citations

 (42)
library_books

A whole genome sequence study identifies genetic risk factors for neuromyelitis optica

2018
PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] included. genes with at least two variants in the mentioned categories were analyzed. five principal components were used as covariates using the logistic wald test implemented as b.collapse in the epacts package. we used a significance threshold of 2.5 × 10−6 to account for ~ 25,000 protein-coding genes in the human genome., variants with mafs > 1% were selected for single-variant […]

library_books

Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey

2018
PMCID: 5886383
PMID: 29621232
DOI: 10.1371/journal.pgen.1007275

[…] were then inverse normal-transformed to satisfy model assumptions of normality. efficient mixed model associations (emmax) accounting for population structure and relatedness were performed using epacts v.3.1.0 []. because emmax was designed for analysis of linear traits, gwa analyses for t2d were performed using the firth bias-corrected logistic regression likelihood ratio test implemented […]

library_books

Evaluation of Gene Based Family Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease

2018
PMCID: 5893779
PMID: 29670507
DOI: 10.3389/fnins.2018.00209

[…] family structure in its gene-based calculations. among the software that can manage large pedigrees we find skat (wu et al., ), fskat (yan et al., ), gskat (wang et al., ), rv-gdt (he et al., ), epacts (http://genome.sph.umich.edu/wiki/epacts), farvat (choi et al., ), pedgene (schaid et al., ), and rareibd (sul et al., )., in this study, we wanted to evaluate the performance of the eight […]

library_books

Genome wide analysis yields new loci associating with aortic valve stenosis

2018
PMCID: 5840367
PMID: 29511194
DOI: 10.1038/s41467-018-03252-6

[…] individuals without a code specific for as. in total, 1,546 cases with as and 24,235 controls genotyped with illumina humancoreexome arrays were analyzed. association analysis were conducted using epacts-3.3. the snp-phenotype associations were modeled using the firth bias-corrected logistic likelihood ratio test, assuming an additive genetic model for genotyped markers and imputed genotypes. […]

library_books

Data on genetic associations of carotid atherosclerosis markers in Mexican American and European American rheumatoid arthritis subjects

2018
PMCID: 5842364
PMID: 29527544
DOI: 10.1016/j.dib.2018.02.006

[…] or = odds ratio., a1 = minor allele., p values ranked from low to high., as shown in , quantile-quantile (q-q) plots of the transformed cimt and plaque in both mas and eas have been generated using epacts. q-q plots exhibited a roughly straight line through the origin with a unit slope indicating almost no inflation.fig. 1fig. 1, to further investigate the genetic architecture of cimt, prs […]

library_books

Whole exome sequencing and gene based rare variant association tests suggest that PLA2G4E might be a risk gene for panic disorder

2018
PMCID: 5804028
PMID: 29391400
DOI: 10.1038/s41398-017-0088-0

[…] g>t in pla2g4e; chr20: 3641457, g>c in gfra4). statistical analyses of these three genes showed that pla2g4e yielded the lowest p value in gene-based rare variant association tests by efficient and parallelizable association container toolbox algorithms; however, the p value did not reach the significance threshold in the japanese. likewise, in a german case–control study (96 […]


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