Package: EZbakR
Title: Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq
        Data
Version: 0.2.2
Authors@R: 
    person(given = "Isaac",
           family = "Vock",
           role = c("aut", "cre", "cph"),
           email = "isaac.vock@gmail.com",
           comment = c(ORCID = "0000-0002-7178-6886"))
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: knitr, MASS, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
biocViews:
Additional_repositories: https://bioconductor.org/packages/release/bioc
Imports: arrow, data.table, dplyr, ggplot2, magrittr, methods, purrr,
        rlang, tidyr, tximport
Depends: R (>= 3.5)
LazyData: true
VignetteBuilder: knitr
URL: https://isaacvock.github.io/EZbakR/,
        https://github.com/isaacvock/EZbakR
BugReports: https://github.com/isaacvock/EZbakR/issues
Config/pak/sysreqs: cmake libicu-dev libssl-dev
Repository: https://isaacvock.r-universe.dev
Date/Publication: 2026-10-13 18:20:51 UTC
RemoteUrl: https://github.com/isaacvock/ezbakr
RemoteRef: HEAD
RemoteSha: 605c4cf2c0f25328ad8ba8d51593f0aa2a860f96
NeedsCompilation: no
Packaged: 2026-10-13 20:46:48 UTC; root
Author: Isaac Vock [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-7178-6886>)
Maintainer: Isaac Vock <isaac.vock@gmail.com>