RFLOMICS

[nbessoltane]

Dear Bioconductor team,

• Repository: https://github.com/RFLOMICS/RFLOMICS

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[bioc-issue-bot]

Hi @nbessoltane

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: RFLOMICS
Title: Interactive web application for Omics-data analysis
Version: 0.99.1
Authors@R: 
    c(
    person(given = "Nadia", family = "Bessoltane",email = "nadia.bessoltane@inrae.fr", role = c("aut", "cre"), comment = c(ORCID="0000-0001-6931-2529")),
    person(given = "Delphine", family = "Charif", email = "delphine.charif@inrae.fr", role = c("aut"), comment = c(ORCID="0000-0002-1949-5969")),
    person(given = "Audrey", family = "Hulot", email = "audrey.hulot@inrae.fr", role = c("aut"), comment = c(ORCID = "0000-0002-9647-6470")),
    person(given = "Christine", family = "Paysant-Leroux", email = "christine.paysant-le-roux@inrae.fr", role = c("aut"), comment = c(ORCID = "0000-0003-2046-6492")),
    person(given = "Gwendal", family = "Cueff", email = "gwendal.cueff@inrae.fr", role = c("aut"))
    )
Description: R-package with shiny interface, provides a framework for the analysis of transcriptomics, proteomics and/or metabolomics data. The interface offers a guided experience for the user, from the definition of the experimental design to the integration of several omics table together. A report can be generated with all settings and analysis results.
URL: https://github.com/RFLOMICS/RFLOMICS
BugReports: https://github.com/RFLOMICS/RFLOMICS/issues
Depends: 
    R (>= 4.4.0),
    SummarizedExperiment,
    MultiAssayExperiment,
    shinyBS,
    knitr
biocViews: ShinyApps, DifferentialExpression, Metabolomics, Proteomics, Transcriptomics
License: Artistic-2.0 
Encoding: UTF-8
RoxygenNote: 7.3.2
Suggests: 
    testthat,
    BiocStyle,
    org.At.tair.db,
    org.Hs.eg.db
VignetteBuilder: knitr
Imports:
    vroom,
    AnnotationDbi,
    circlize,
    clusterProfiler,
    ComplexHeatmap,
    coseq,
    data.table,
    dplyr,
    DT,
    edgeR,
    EnhancedVolcano,
    enrichplot,
    FactoMineR,
    ggplot2,
    ggpubr,
    ggrepel,
    grDevices,
    grid,
    gridExtra,
    htmltools,
    limma,
    magrittr,
    methods,
    mixOmics,
    MOFA2,
    pathview,
    png,
    purrr,
    RColorBrewer,
    reshape2,
    reticulate,
    rmarkdown,
    S4Vectors,
    shiny,
    shinydashboard,
    shinyWidgets,
    stats,
    stringr,
    tidyr,
    tibble,
    tidyselect,
    UpSetR,
    utils,
    httr

[lshep]

general

• [ ] Your git direcotry should not include a renv directory and renv.lock. We would also prefer Dockerfiles and pkgdown sites not to be checked into Bioconductor. Please move to another branch on github before we check the package into our git repository.

vignettes

• [ ] Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope.

• [ ] The vignette RFLOMICS-cmd-line is unfinished and either should not be included or should be a completed vignette.

• [ ] Currently your vignettes are not adequate for Bioconductor. None of your vignettes have runable code. They are screenshots or your runable code is displaying your premade data object.

data/input

• [ ] I see your data object is a bunch of data.frames. Does your package also take standard Bioconductor input such as a SummarizedExperiment/MultiAssayExperiment for assay data or Spectra for proteomics?