Package: STADyUM
Type: Package
Title: Statistical Transcriptome Analysis under a Dynamic Unified Model
Version: 0.99.4
Authors@R: 
    c(
        person("Yixin", "Zhao", 
            email = "",
            role = c("aut"),
            comment = c(ORCID = "0000-0002-7856-2818")
        ),
        person("Lingjie", "Liu",
            email = "",
            role = c("aut"),
            comment = c(ORCID = "0000-0002-5765-1213")
        ),
        person("Rebecca", "Hassett",
            email = "hassett@cshl.edu",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5133-9387")
        )
    )
Description: STADyUM is a package with functionality for analyzing nascent
    RNA read counts to infer transcription rates. This includes utilities for
    processing experimental nascent RNA read counts as well as for simulating 
    PRO-seq data. Rates such as initiation, pause release and landing pad 
    occupancy are estimated from either synthetic or experimental data. There 
    are also options for varying pause sites and including steric hindrance of
    initiation in the model.
URL: https://github.com/rhassett-cshl/STADyUM
BugReports: https://github.com/rhassett-cshl/STADyUM
biocViews: StatisticalMethod, Transcriptomics, Transcription,
        Sequencing
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: GenomicRanges, IRanges, S4Vectors, methods, tibble, dplyr,
        ggplot2, progress, plyranges, GenomeInfoDb, Rcpp, data.table,
        purrr, rtracklayer, tidyr, rlang, MASS
LinkingTo: Rcpp
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends: R (>= 4.5.0)
git_url: https://git.bioconductor.org/packages/STADyUM
git_branch: devel
git_last_commit: b71dd9e
git_last_commit_date: 2025-10-12
Repository: Bioconductor 3.22
Date/Publication: 2025-10-16
NeedsCompilation: yes
Packaged: 2025-10-17 00:07:12 UTC; biocbuild
Author: Yixin Zhao [aut] (ORCID: <https://orcid.org/0000-0002-7856-2818>),
  Lingjie Liu [aut] (ORCID: <https://orcid.org/0000-0002-5765-1213>),
  Rebecca Hassett [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5133-9387>)
Maintainer: Rebecca Hassett <hassett@cshl.edu>
Built: R 4.5.1; x86_64-apple-darwin20; 2025-10-17 08:17:53 UTC; unix
