Tree-based differential testing using inferential uncertainty for RNA-Seq.

ABSTRACT: Identifying differentially expressed transcripts poses a crucial yet challenging problem in transcriptomics. Substantial uncertainty is associated with the abundance estimates of certain transcripts which, if ignored, can lead to the exaggeration of false positives and, if included, may lead to reduced power. Given a set of RNA-Seq samples, TreeTerminus arranges transcripts in a hierarchical tree structure that encodes different layers of resolution for interpretation of the abundance of transcriptional groups, with uncertainty generally decreasing as one ascends the tree from the leaves. We introduce mehenDi, which utilizes the tree structure from TreeTerminus for differential testing. The nodes output by mehenDi, called the selected nodes are determined in a data-driven manner to maximiz

SUBMITTER: Singh NP 

PROVIDER: S-EPMC10793400 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature