EZbakR - Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq Data

A complete rewrite and reimagining of 'bakR' (see 'Vock et al.' (2025) <doi:10.1371/journal.pcbi.1013179>). Designed to support a wide array of analyses of nucleotide recoding RNA-seq (NR-seq) datasets of any type, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq), TT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR' extends standard NR-seq standard NR-seq mutational modeling to support multi-label analyses (e.g., 4sU and 6sG dual labeling), and implements an improved hierarchical model to better account for transcript-to-transcript variance in metabolic label incorporation. 'EZbakR' also generalized dynamical systems modeling of NR-seq data to support analyses of premature mRNA processing and flow between subcellular compartments. Finally, 'EZbakR' implements flexible and well-powered comparative analyses of all estimated parameters via design matrix-specified generalized linear modeling.