LmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models.

ABSTRACT:

Background

Studies that utilize RNA Sequencing (RNA-Seq) in conjunction with designs that introduce dependence between observations (e.g. longitudinal sampling) require specialized analysis tools to accommodate this additional complexity. This R package contains a set of utilities to fit linear mixed effects models to transformed RNA-Seq counts that properly account for this dependence when performing statistical analyses.

Results

In a simulation study comparing lmerSeq and two existing methodologies that also work with transformed RNA-Seq counts, we found that lmerSeq was comprehensively better in terms of nominal error rate control and statistical power.

Conclusions

Existing R packages for analyzing transformed RNA-Seq data with linear mixed models are limited in th

SUBMITTER: Vestal BE 

PROVIDER: S-EPMC9670578 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature