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LIMIX specifications


Unique identifier OMICS_27082
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Version 1.0.12
Stability Stable
Maintained Yes




No version available



  • person_outline Oliver Stegle
  • person_outline Christoph Lippert

Additional information

Publication for LIMIX

LIMIX citations


Interactions between genetic variation and cellular environment in skeletal muscle gene expression

PLoS One
PMCID: 5901994
PMID: 29659628
DOI: 10.1371/journal.pone.0195788

[…] gical effects []. We additionally include age and sex as covariates when either trait was not considered as an environmental trait. We implemented the GxE model using the linear mixed model framework LIMIX (v0.7.6) [,].We combined the ASE p-values and gene expression p-values using Fisher’s combined test. We controlled for FDR per environment using the Benjamini–Hochberg procedure []. Our method a […]


The maternal environment interacts with genetic variation in regulating seed dormancy in Swedish Arabidopsis thaliana

PLoS One
PMCID: 5744996
PMID: 29281703
DOI: 10.1371/journal.pone.0190242

[…] The variance component analysis was described earlier in []. It was carried out in LIMIX [] using the following model: Y=[μwarm,μcold]⊗1N,1+Uglobal+ψ(2) where μwarm and μcold are environment specific mean values, Uglobal is a matrix of global relatedness fitted as random effect, and […]


Polygenicity and Epistasis Underlie Fitness Proximal Traits in the Caenorhabditis elegans Multiparental Experimental Evolution (CeMEE) Panel

PMCID: 5714472
PMID: 29066469
DOI: 10.1534/genetics.117.300406

[…] , with A the n×n GSM from the most predictive additive fit found for each trait, and e is residual error. The above model was compared to a null model excluding genotype effects by LRT (fit using the LIMIX Python package, GWAS P-values for size and fertility are in File S14, using genetic similarities in File S15 and File S16.To assess the mapping resolution and po […]


Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N glycosylation

Nat Commun
PMCID: 5587582
PMID: 28878392
DOI: 10.1038/s41467-017-00453-3

[…] ulation structure does. In such situations, the method of choice is mixed effect models; however, a fast mixed model analysis for multiple (more than tens of) phenotypes is still difficult. GEMMA and Limix were designed to overcome such difficulty, although the computational cost can be high for a large number of phenotypes such as that encountered in omics data. Another difficulty faced in multiv […]


Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

Cell Rep
PMCID: 5583477
PMID: 28854368
DOI: 10.1016/j.celrep.2017.08.010

[…] ein and mRNA abundances. Volcano plots, boxplots, distribution plots, scatterplots, and bar plots were drawn in RStudio with the ggplot2 and ggrepel packages. All QTL associations were implemented by LIMIX using a linear regression test. […]


Genetic Variation in the Social Environment Contributes to Health and Disease

PLoS Genet
PMCID: 5266220
PMID: 28121987
DOI: 10.1371/journal.pgen.1006498

[…] For each trait, Eq () was used to partition phenotypic variance into its individual components. All models were fitted using LIMIX[, ], which we extended to handle models with correlated variance components. The model was fitted using restricted maximum likelihood (REML). We report the contribution of DGE and SGE to phenoty […]


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LIMIX institution(s)
Microsoft Research, Los Angeles, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK; Machine Learning and Computational Biology Research Group, Max Planck Institutes, Tubingen, Germany
LIMIX funding source(s)
Supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with the Broad Institute, UCLA, University of Oulu, and the National Institute for Health and Welfare in Finland.

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