bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling

• Published in: RNA (Cambridge) Vol. 29; no. 7; pp. 958 - 976
• Main Authors: Vock, Isaac W, Simon, Matthew D
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.07.2023
• Subjects: Bayes Theorem; Bayesian analysis; Bioinformatics; Degradation; Gene Expression Profiling - methods; Kinetics; Mathematical models; RNA - genetics; Sequence Analysis, RNA - methods; Software; Statistical analysis; Transcription; Transcriptome; Transcriptomes; Bayesian hierarchical modeling; RNA metabolic labeling; RNA kinetics; TimeLapse-seq; SLAM-seq

Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in cellular RNA levels, but provides limited information about the kinetic mechanisms underlying such changes. Nucleotide recoding RNA-seq methods (NR-seq; e.g., TimeLapse-seq, SLAM-seq, etc.) address this shortco...