EPACTS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool EPACTS

Tool usage distribution map

This map represents all the scientific publications referring to EPACTS per scientific context
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Associated diseases

This word cloud represents EPACTS usage per disease context

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EPACTS specifications


Unique identifier OMICS_07453
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




No version available


Additional information


EPACTS citations


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

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

[…] e 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. […]


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

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

[…] als 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 in […]


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

Front Neurosci
PMCID: 5893779
PMID: 29670507
DOI: 10.3389/fnins.2018.00209

[…] mplemented in the R package SKATv2. The four kinship matrices tested were pedigree calculation (PED), Identity By State (IBS) estimation, Balding-Nichols (BN) estimation, and the kinship generated by EPACTS (HR) which is also based on the BN algorithm (Figure ). Table offers a comparison of these kinships for FAM#1 and FAM#2 of our simulated dataset. For these analyses, we ran the SKAT-EMMAX meth […]


Genome wide analysis yields new loci associating with aortic valve stenosis

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

[…] ll 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. M […]


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

PMCID: 5842364
PMID: 29527544
DOI: 10.1016/j.dib.2018.02.006
call_split See protocol

[…] alues (y –axis) versus the quantile distribution of expected (normal or theoretical) chi-squared values (x –axis) graphically by plotting their quantiles against each other. Q-Q plots were done using Efficient and Parallelizable Association Container Toolbox software [EPACTS, http://genome.sph.umich.edu/wiki/EPACTS]. Association p values were adjusted for multiple testing using the conservative Bo […]


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

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

[…] To test differences in the mutational burden of the candidate genes, we used Efficient and Parallelizable Association Container Toolbox (EPACTS). In the EPACTS algorithms, we used three different analyses (CMC, Madsen–Browning, and SKAT-O). We removed common variants using the […]

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