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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.

Version: 0.1.0
Depends: R (≥ 3.5)
Imports: arrow, data.table, dplyr, ggplot2, magrittr, methods, purrr, rlang, tidyr, tximport
Suggests: knitr, MASS, rmarkdown, testthat (≥ 3.0.0)
Published: 2025-12-10
DOI: 10.32614/CRAN.package.EZbakR
Author: Isaac Vock ORCID iD [aut, cre, cph]
Maintainer: Isaac Vock <isaac.vock at gmail.com>
BugReports: https://github.com/isaacvock/EZbakR/issues
License: MIT + file LICENSE
URL: https://isaacvock.github.io/EZbakR/, https://github.com/isaacvock/EZbakR
NeedsCompilation: no
Materials: README, NEWS
CRAN checks: EZbakR results

Documentation:

Reference manual: EZbakR.html , EZbakR.pdf
Vignettes: EZDynamics (source, R code)
EZQC (source, R code)
EZget (source, R code)
EstimateFractions (source, R code)
EstimateKinetics (source, R code)
Linear-modeling (source, R code)
Quickstart (source, R code)

Downloads:

Package source: EZbakR_0.1.0.tar.gz
Windows binaries: r-devel: EZbakR_0.1.0.zip, r-release: not available, r-oldrel: EZbakR_0.1.0.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): EZbakR_0.1.0.tgz, r-oldrel (x86_64): EZbakR_0.1.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=EZbakR to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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