Package: dearseq
Type: Package
Title: Differential Expression Analysis for RNA-seq data through a
        robust variance component test
Version: 1.22.0
Date: 2023-06-16
Authors@R: c(person("Denis", "Agniel", role = c("aut"),
                    email = "denis.agniel@gmail.com"),
	           person("Boris P.", "Hejblum", role = c("aut", "cre"),
	                  email = "boris.hejblum@u-bordeaux.fr",
	                  comment = c(ORCID="0000-0003-0646-452X")),
	           person("Marine", "Gauthier", role = c("aut"),
	                  email = "marine.gauthier@u-bordeaux.fr"),
	           person("Mélanie", "Huchon", role = c("ctb"),
	                  email = "melanie.huchon@u-bordeaux.fr"))
Depends: R (>= 3.6.0)
Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr,
        matrixStats, methods, patchwork, parallel, pbapply, reshape2,
        rlang, scattermore, stats, statmod, survey, tibble, viridisLite
Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
        knitr, limma, readxl, rmarkdown, S4Vectors,
        SummarizedExperiment, testthat, covr
Description: Differential Expression Analysis RNA-seq data with
        variance component score test accounting for data
        heteroscedasticity through precision weights. Perform both
        gene-wise and gene set analyses, and can deal with repeated or
        longitudinal data. Methods are detailed in: i) Agniel D &
        Hejblum BP (2017) Variance component score test for time-course
        gene set analysis of longitudinal RNA-seq data, Biostatistics,
        18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R &
        Hejblum BP (2020) dearseq: a variance component score test for
        RNA-Seq differential analysis that effectively controls the
        false discovery rate, NAR Genomics and Bioinformatics,
        2(4):lqaa093.
License: GPL-2 | file LICENSE
biocViews: BiomedicalInformatics, CellBiology, DifferentialExpression,
        DNASeq, GeneExpression, Genetics, GeneSetEnrichment,
        ImmunoOncology, KEGG, Regression, RNASeq, Sequencing,
        SystemsBiology, TimeCourse, Transcription, Transcriptomics
BugReports: https://github.com/borishejblum/dearseq/issues
Encoding: UTF-8
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Config/pak/sysreqs: make libicu-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:56:12 UTC
RemoteUrl: https://github.com/bioc/dearseq
RemoteRef: RELEASE_3_22
RemoteSha: f876c6d88d67bcfdc91eba4a1010990eb03a1448
NeedsCompilation: no
Packaged: 2025-11-11 13:59:14 UTC; root
Author: Denis Agniel [aut],
  Boris P. Hejblum [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0646-452X>),
  Marine Gauthier [aut],
  Mélanie Huchon [ctb]
Maintainer: Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
Built: R 4.5.2; ; 2025-11-11 14:08:25 UTC; windows
