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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "STADyUM" in publications use:'
type: software
license: MIT
title: 'STADyUM: Statistical Transcriptome Analysis under a Dynamic Unified Model'
version: 1.3.0
doi: 10.1093/nar/gkad843
identifiers:
- type: doi
  value: 10.32614/CRAN.package.STADyUM
abstract: 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.
authors:
- family-names: Zhao
  given-names: Yixin
  orcid: https://orcid.org/0000-0002-7856-2818
- family-names: Liu
  given-names: Lingjie
  orcid: https://orcid.org/0000-0002-5765-1213
- family-names: Hassett
  given-names: Rebecca
  email: hassett@cshl.edu
  orcid: https://orcid.org/0000-0001-5133-9387
preferred-citation:
  type: article
  title: STADyUM
  authors:
  - family-names: Zhao
    given-names: Yixin
    orcid: https://orcid.org/0000-0002-7856-2818
  - family-names: Liu
    given-names: Lingjie
    orcid: https://orcid.org/0000-0002-5765-1213
  - family-names: Hassett
    given-names: Rebecca
    email: hassett@cshl.edu
    orcid: https://orcid.org/0000-0001-5133-9387
  - family-names: Siepel
    given-names: Adam
  journal: Nucleic Acids Research
  year: '2023'
  volume: '51'
  issue: '21'
  doi: 10.1093/nar/gkad843
  start: e106
repository: https://bioc.r-universe.dev
repository-code: https://github.com/rhassett-cshl/STADyUM
commit: 7cb7fa1711d88e5589cdb8cf023131bd8c718c38
url: https://github.com/rhassett-cshl/STADyUM
date-released: '2026-04-28'
contact:
- family-names: Hassett
  given-names: Rebecca
  email: hassett@cshl.edu
  orcid: https://orcid.org/0000-0001-5133-9387