Statistical approaches for differential expression analysis in metatranscriptomics.

ABSTRACT:

Motivation

Metatranscriptomics (MTX) has become an increasingly practical way to profile the functional activity of microbial communities in situ. However, MTX remains underutilized due to experimental and computational limitations. The latter are complicated by non-independent changes in both RNA transcript levels and their underlying genomic DNA copies (as microbes simultaneously change their overall abundance in the population and regulate individual transcripts), genetic plasticity (as whole loci are frequently gained and lost in microbial lineages) and measurement compositionality and zero-inflation. Here, we present a systematic evaluation of and recommendations for differential expression (DE) analysis in MTX.

Results

We designed and assessed six statistical models fo

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC8275336 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature