Package: DOTSeq
Type: Package
Title: Differential Analysis of Translation Efficiency and Usage of
        Open Reading Frames
Version: 0.99.4
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")
        ),
    person(
        "Marsden", 
        role="fnd"
        )
    )
Description: 
    A flexible beta-binomial generalized linear model (GLM) framework for 
    modeling the expected proportion of ribosome profiling (Ribo-seq) to 
    RNA-seq counts for individual open reading frames (ORFs) relative to 
    other ORFs within the same gene. This is complemented by a negative 
    binomial GLM framework that captures changes in translation efficiency 
    of individual ORFs across experimental conditions.
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, pasillaBamSubset,
        BiocStyle, biomaRt, DHARMa, eulerr, ggplot2, ggsignif, knitr,
        rmarkdown, testthat, withr
Imports: ashr, boot, data.table, emmeans, glmmTMB, methods, Rcpp,
        stats, utils, graphics, grDevices, pbapply, AnnotationDbi,
        BiocGenerics, Biostrings, BSgenome, txdbmaker, DESeq2,
        GenomicAlignments, GenomicFeatures, GenomeInfoDb,
        GenomeInfoDbData, GenomicRanges, IRanges, rtracklayer,
        Rsamtools, S4Vectors, SummarizedExperiment
biocViews: GeneRegulation, GeneExpression, DifferentialExpression,
        Genetics, Sequencing, Software, RNASeq, Bayesian, Regression,
        MultipleComparison
License: MIT + file LICENSE
git_url: https://git.bioconductor.org/packages/DOTSeq
git_branch: devel
git_last_commit: c898885
git_last_commit_date: 2025-11-30
Repository: Bioconductor 3.23
Date/Publication: 2026-01-13
NeedsCompilation: yes
Packaged: 2026-01-13 22:31:00 UTC; biocbuild
Author: Chun Shen Lim [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7015-0125>),
  Gabrielle Chieng [aut, ctb],
  Marsden [fnd]
Maintainer: Chun Shen Lim <lim.bioinfo@gmail.com>
