Package: MultiRNAflow
Title: An R package for integrated analysis of temporal RNA-seq data
        with multiple biological conditions
Version: 1.9.0
Authors@R: c(
    person("Rodolphe", "Loubaton", , "loubaton.rodolphe@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-1442-7270")),
    person("Nicolas", "Champagnat", , "nicolas.champagnat@inria.fr", role = c("aut", "ths"),
           comment = c(ORCID = "0000-0002-5128-2357")),
    person("Laurent", "Vallat", , "vallat@unistra.fr", role = c("aut", "ths"),
           comment = c(ORCID = "0000-0002-5226-7706")),
    person("Pierre", "Vallois", , "pierre.vallois@univ-lorraine.fr", role = "aut",
           comment = c(ORCID = "0000-0002-2123-0142")),
    person("Région Grand Est", role = "fnd"),
    person("Cancéropôle Est", role = "fnd")
  )
Description: Our R package MultiRNAflow provides an easy to use unified
        framework allowing to automatically make both unsupervised and
        supervised (DE) analysis for datasets with an arbitrary number
        of biological conditions and time points.  In particular, our
        code makes a deep downstream analysis of DE information, e.g.
        identifying temporal patterns across biological conditions and
        DE genes which are specific to a biological condition for each
        time.
License: GPL-3 | file LICENSE
URL: https://github.com/loubator/MultiRNAflow
BugReports: https://github.com/loubator/MultiRNAflow/issues
Depends: Mfuzz (>= 2.64.0), R (>= 4.4)
Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.20.0), DESeq2 (>=
        1.44.0), factoextra (>= 1.0.7), FactoMineR (>= 2.11),
        ggalluvial (>= 0.12.5), ggplot2 (>= 3.5.1), ggplotify (>=
        0.1.2), ggrepel (>= 0.9.5), gprofiler2 (>= 0.2.3), graphics (>=
        4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>=
        1.4.1), plot3Drgl (>= 1.0.4), reshape2 (>= 1.4.4), rlang (>=
        1.1.6), S4Vectors (>= 0.42.0), stats (>= 4.2.2),
        SummarizedExperiment (>= 1.34.0), UpSetR (>= 1.4.0), utils (>=
        4.2.2)
Suggests: BiocGenerics (>= 0.40.0), BiocStyle (>= 2.32.1), e1071 (>=
        1.7.12), knitr (>= 1.47), rmarkdown (>= 2.27), testthat (>=
        3.0.0)
VignetteBuilder: knitr
biocViews: Sequencing, RNASeq, GeneExpression, Transcription,
        TimeCourse, Preprocessing, Visualization, Normalization,
        PrincipalComponent, Clustering, DifferentialExpression,
        GeneSetEnrichment, Pathways
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/pak/sysreqs: cmake libfreetype6-dev libglu1-mesa-dev make
        texlive libicu-dev libpng-dev libgl1-mesa-dev libssl-dev perl
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:24:54 UTC
RemoteUrl: https://github.com/bioc/MultiRNAflow
RemoteRef: HEAD
RemoteSha: 3c2e28d2b106cfc7749089257f2953963e77b0c8
NeedsCompilation: no
Packaged: 2026-02-21 07:22:14 UTC; root
Author: Rodolphe Loubaton [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1442-7270>),
  Nicolas Champagnat [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-5128-2357>),
  Laurent Vallat [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-5226-7706>),
  Pierre Vallois [aut] (ORCID: <https://orcid.org/0000-0002-2123-0142>),
  Région Grand Est [fnd],
  Cancéropôle Est [fnd]
Maintainer: Rodolphe Loubaton <loubaton.rodolphe@gmail.com>
Built: R 4.6.0; ; 2026-02-21 07:25:21 UTC; windows
