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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:06:05 UTC
RemoteUrl: https://github.com/bioc/DOTSeq
RemoteRef: RELEASE_3_23
RemoteSha: 7717b3ef594d5cdd2c20700bba32f4e38091cb8f
NeedsCompilation: yes
Packaged: 2026-04-29 21:08:31 UTC; root
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>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-04-29 21:16:10 UTC; windows
Archs: x64
