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 (may not be active yet) |
| Author: | Isaac Vock  [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: not available |
| 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:
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