Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq Data R package EZbakR version 0.1.0 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. Software Depends: R (>= 3.5) Imports: arrow, data.table, dplyr, ggplot2, magrittr, methods, purrr, rlang, tidyr, tximport Suggests: knitr, MASS, rmarkdown, testthat (>= 3.0.0) Isaac Vock <isaac.vock@gmail.com> Comprehensive R Archive Network (CRAN) Isaac Vock [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-7178-6886>) MIT + file LICENSE (https://CRAN.R-project.org/package=EZbakR/LICENSE) 2025-12-10 application/tgz https://CRAN.R-project.org/package=EZbakR doi:10.32614/CRAN.package.EZbakR