EZbakR
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 anytype, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq),TT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR' extendsstandard 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 betteraccount for transcript-to-transcript variance in metabolic label incorporation.'EZbakR' also generalized dynamical systems modeling of NR-seq data to support analysesof premature mRNA processing and flow between subcellular compartments. Finally,'EZbakR' implements flexible and well-powered comparative analyses of allestimated parameters via design matrix-specified generalized linear modeling.
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