Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data.

ABSTRACT:

Motivation

The identification of differentially expressed genes (DEGs) from transcriptomic datasets is a major avenue of research across diverse disciplines. However, current bioinformatic tools do not support covariance matrices in DEG modeling. Here, we introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling including covariates, weights, random effects, covariance matrices, and fit metrics.

Results

In simulated datasets, kimma detects DEGs with similar specificity, sensitivity, and computational time as limma unpaired and dream paired models. Unlike other software, kimma supports covariance matrices as well as fit metrics like Akaike information criterion (AIC). Utilizing genetic kinship covariance, kimma reve

SUBMITTER: Dill-McFarland KA 

PROVIDER: S-EPMC10182851 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature