Package: STADyUM
Type: Package
Title: Statistical Transcriptome Analysis under a Dynamic Unified Model
Version: 1.3.2
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")
        ),
        person("Xin", "Zeng",
            email = "zeng@cshl.edu",
            role = c("aut", "aut")
        )
    )
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, Preprocessing
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: GenomicRanges, IRanges, S4Vectors, methods, tibble, dplyr,
        ggplot2, progress, GenomeInfoDb, Rcpp, data.table, purrr,
        rtracklayer, tidyr, rlang, MASS, plyranges, pracma,
        ggpointdensity, BiocFileCache
LinkingTo: Rcpp
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, devtools, ggpubr,
        cowplot
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends: R (>= 4.5.0)
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-22 22:48:34 UTC
RemoteUrl: https://github.com/bioc/STADyUM
RemoteRef: HEAD
RemoteSha: 5006f5643eed80a27418d84dae8f201c41a2fed1
NeedsCompilation: yes
Packaged: 2026-06-23 06:56:31 UTC; root
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>),
  Xin Zeng [aut, aut]
Maintainer: Rebecca Hassett <hassett@cshl.edu>