Package: compcodeR
Type: Package
Title: RNAseq data simulation, differential expression analysis and
        performance comparison of differential expression methods
Version: 1.49.0
Authors@R: c(
    person("Charlotte", "Soneson", role = c("aut", "cre"), 
           email = "charlottesoneson@gmail.com", comment = c(ORCID = "0000-0003-3833-2169")),
    person("Paul", "Bastide", role = "aut",
           email = "paul.bastide@umontpellier.fr", comment = c(ORCID = "0000-0002-8084-9893")),
    person("Mélina", "Gallopin", role = "aut",
           email = "melina.gallopin@u-psud.fr", comment = c(ORCID = "0000-0002-2431-7825 "))
           )
Description: This package provides extensive functionality for
        comparing results obtained by different methods for
        differential expression analysis of RNAseq data. It also
        contains functions for simulating count data. Finally, it
        provides convenient interfaces to several packages for
        performing the differential expression analysis. These can also
        be used as templates for setting up and running a user-defined
        differential analysis workflow within the framework of the
        package.
Depends: R (>= 4.0), sm
Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots,
        gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr,
        modeest, edgeR, limma, vioplot, methods, stats, utils, ape,
        phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny,
        shinydashboard
Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq,
        TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree,
        tidytree, statmod, covr, sva, tcltk
Enhances: rpanel, DSS
License: GPL (>= 2)
VignetteBuilder: knitr
biocViews: ImmunoOncology, RNASeq, DifferentialExpression
RoxygenNote: 7.2.3
URL: https://github.com/csoneson/compcodeR
BugReports: https://github.com/csoneson/compcodeR/issues
Encoding: UTF-8
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:39:02 UTC
RemoteUrl: https://github.com/bioc/compcodeR
RemoteRef: HEAD
RemoteSha: 734da123619997b3967395a3ee00f9e26072f217
NeedsCompilation: no
Packaged: 2026-05-31 06:39:14 UTC; root
Author: Charlotte Soneson [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3833-2169>),
  Paul Bastide [aut] (ORCID: <https://orcid.org/0000-0002-8084-9893>),
  Mélina Gallopin [aut] (ORCID: <https://orcid.org/0000-0002-2431-7825>)
Maintainer: Charlotte Soneson <charlottesoneson@gmail.com>