Package: DOTSeq
Type: Package
Title: Genome-wide Detection of Differential ORF Usage
Version: 1.0.0
Authors@R: c(
    person(
        given = "Chun Shen", 
        family = "Lim", 
        email="lim.bioinfo@gmail.com", 
        role = c("aut","cre"), 
        comment = c(ORCID = "0000-0001-7015-0125")
        ),
    person(
        given = "Gabrielle", 
        family = "Chieng", 
        role = c("aut","ctb"),
        comment = c(ORCID = "0009-0008-8710-9979")
        ),
    person(
        "Marsden", 
        role="fnd"
        )
    )
Description: 
    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.
URL: https://github.com/compgenom/DOTSeq
BugReports: https://github.com/compgenom/DOTSeq/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
VignetteBuilder: knitr
LinkingTo: Rcpp
Suggests: BSgenome.Hsapiens.UCSC.hg38,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Dmelanogaster.UCSC.dm3.ensGene, org.Hs.eg.db, curl,
        pasillaBamSubset, BiocStyle, biomaRt, DHARMa, eulerr, ggplot2,
        ggsignif, knitr, rmarkdown, testthat, withr, magick
Imports: ashr, boot, data.table, emmeans, glmmTMB, Matrix, methods,
        Rcpp, stats, utils, graphics, grDevices, pbapply,
        AnnotationDbi, BiocGenerics, BiocParallel, Biostrings,
        BSgenome, txdbmaker, DESeq2, GenomicAlignments,
        GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicRanges,
        IRanges, rtracklayer, Rsamtools, S4Vectors,
        SummarizedExperiment
biocViews: RiboSeq, SingleCell, GeneRegulation, GeneExpression,
        DifferentialExpression, Genetics, Sequencing, Software, RNASeq,
        Bayesian, Regression, MultipleComparison
License: MIT + file LICENSE
git_url: https://git.bioconductor.org/packages/DOTSeq
git_branch: RELEASE_3_23
git_last_commit: 7717b3e
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: yes
Packaged: 2026-04-28 21:55:25 UTC; biocbuild
Author: Chun Shen Lim [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7015-0125>),
  Gabrielle Chieng [aut, ctb] (ORCID:
    <https://orcid.org/0009-0008-8710-9979>),
  Marsden [fnd]
Maintainer: Chun Shen Lim <lim.bioinfo@gmail.com>
