Package: MultiRNAflow
Title: An R package for integrated analysis of temporal RNA-seq data
        with multiple biological conditions
Version: 1.5.0
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 (>= 2.58.0), R (>= 4.3)
Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.14.0), DESeq2 (>=
        1.38.1), factoextra (>= 1.0.7), FactoMineR (>= 2.6), ggalluvial
        (>= 0.12.3), ggplot2 (>= 3.4.0), ggplotify (>= 0.1.2), ggrepel
        (>= 0.9.2), gprofiler2 (>= 0.2.1), graphics (>= 4.2.2),
        grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4),
        plot3Drgl (>= 1.0.3), reshape2 (>= 1.4.4), S4Vectors (>=
        0.36.2), stats (>= 4.2.2), SummarizedExperiment (>= 1.28.0),
        UpSetR (>= 1.4.0), utils (>= 4.2.2)
Suggests: BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12),
        knitr, rmarkdown, 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: 7.2.3
git_url: https://git.bioconductor.org/packages/MultiRNAflow
git_branch: devel
git_last_commit: 63c2461
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.21
Date/Publication: 2025-03-05
NeedsCompilation: no
Packaged: 2025-03-05 22:11:42 UTC; biocbuild
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 4.5.0; ; 2025-03-06 03:28:49 UTC; unix
