Package: DRIMSeq
Type: Package
Title: Differential transcript usage and tuQTL analyses with
        Dirichlet-multinomial model in RNA-seq
Version: 1.41.4
Date: 2026-10-29
Authors@R: c(person(given = "Malgorzata", family = "Nowicka",
                    role = c("aut"), email = "gosia.nowicka.uzh@gmail.com"),
             person("Mark D.", "Robinson", role = c("cre"),
                    email = "mark.robinson@mls.uzh.ch",
                    comment = c(ORCID = "0000-0002-3048-5518")))
Description: The package provides two frameworks. One for the
        differential transcript usage analysis between different
        conditions and one for the tuQTL analysis. Both are based on
        modeling the counts of genomic features (i.e., transcripts)
        with the Dirichlet-multinomial distribution. The package also
        makes available functions for visualization and exploration of
        the data and results.
biocViews: ImmunoOncology, SNP, AlternativeSplicing,
        DifferentialSplicing, Genetics, RNASeq, Sequencing,
        WorkflowStep, MultipleComparison, GeneExpression,
        DifferentialExpression
License: GPL (>= 3)
Depends: R (>= 3.4.0)
Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
        BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
        reshape2
Suggests: grid, BiocStyle, knitr, testthat
ByteCompile: false
VignetteBuilder: knitr
Collate: 'DRIMSeq.R' 'aaa.R' 'class_show_utils.R' 'class_MatrixList.R'
        'class_dmDSdata.R' 'class_dmDSprecision.R' 'class_dmDSfit.R'
        'class_dmDStest.R' 'class_dmSQTLdata.R'
        'class_dmSQTLprecision.R' 'class_dmSQTLfit.R'
        'class_dmSQTLtest.R' 'dmDS_CRadjustment.R'
        'dmDS_estimateCommonPrecision.R'
        'dmDS_estimateTagwisePrecision.R' 'dmDS_filter.R' 'dmDS_fit.R'
        'dmDS_profileLik.R' 'dmSQTL_CRadjustment.R'
        'dmSQTL_estimateCommonPrecision.R'
        'dmSQTL_estimateTagwisePrecision.R' 'dmSQTL_filter.R'
        'dmSQTL_fit.R' 'dmSQTL_permutations.R' 'dmSQTL_profileLik.R'
        'dm_CRadjustmentManyGroups.R' 'dm_CRadjustmentOneGroup.R'
        'dm_CRadjustmentRegression.R' 'dm_LRT.R' 'dm_core_Hessian.R'
        'dm_core_colorb.R' 'dm_core_deviance.R' 'dm_core_lik.R'
        'dm_core_score.R' 'dm_estimateMeanExpression.R'
        'dm_fitManyGroups.R' 'dm_fitOneGroup.R' 'dm_fitRegression.R'
        'dm_plotData.R' 'dm_plotPrecision.R' 'dm_plotProportions.R'
        'dm_plotPvalues.R' 'dm_profileLikModeration.R'
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libicu-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-29 17:56:34 UTC
RemoteUrl: https://github.com/bioc/DRIMSeq
RemoteRef: HEAD
RemoteSha: d7a601b2e9a568e89c3e2ed0fe1207b3456ff075
NeedsCompilation: no
Packaged: 2026-10-30 02:13:41 UTC; root
Author: Malgorzata Nowicka [aut],
  Mark D. Robinson [cre] (ORCID: <https://orcid.org/0000-0002-3048-5518>)
Maintainer: Mark D. Robinson <mark.robinson@mls.uzh.ch>