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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 "DOTSeq" in publications use:'
type: software
license: MIT
title: 'DOTSeq: Genome-wide Detection of Differential ORF Usage'
version: 1.1.0
doi: 10.1101/2025.09.24.678201
identifiers:
- type: doi
  value: 10.32614/CRAN.package.DOTSeq
abstract: Differential open reading frame (ORF) translation analysis framework for
  ribosome profiling (Ribo-seq) with matched RNA-seq. Implements (i) Differential
  ORF Usage (DOU), a beta-binomial generalized linear model that models the expected
  proportion of Ribo-seq versus RNA-seq reads mapping to each ORF within a gene, and
  (ii) ORF-level Differential Translation Efficiency (DTE), a negative binomial GLM
  that capture changes in translation efficiency of individual ORFs across experimental
  conditions. Supports ORF-level read summarization for bulk and single-cell Ribo-seq.
authors:
- family-names: Lim
  given-names: Chun Shen
  email: lim.bioinfo@gmail.com
  orcid: https://orcid.org/0000-0001-7015-0125
- family-names: Chieng
  given-names: Gabrielle
  orcid: https://orcid.org/0009-0008-8710-9979
preferred-citation:
  type: article
  title: DOTSeq enables genome-wide detection of differential ORF usage
  authors:
  - family-names: Lim
    given-names: Chun Shen
    email: lim.bioinfo@gmail.com
    orcid: https://orcid.org/0000-0001-7015-0125
  - family-names: Chieng
    given-names: Gabrielle SW
  journal: bioRxiv
  year: '2026'
  publisher:
    name: Cold Spring Harbor Laboratory
  doi: 10.1101/2025.09.24.678201
  start: '2026'
  end: '03'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/compgenom/DOTSeq
commit: 8d37873b5e61305cc47f44c11a05b542a0f5763a
url: https://github.com/compgenom/DOTSeq
date-released: '2026-04-28'
contact:
- family-names: Lim
  given-names: Chun Shen
  email: lim.bioinfo@gmail.com
  orcid: https://orcid.org/0000-0001-7015-0125