New Package Submission: BreastSubtypeR

[yqkiuo]

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• Repository: https://github.com/yqkiuo/BreastSubtypeR

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[bioc-issue-bot]

Hi @yqkiuo

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: BreastSubtypeR
Type: Package
Title: Methods for breast cancer intrinsic subtyping
Description: BreastSubtypeR is an R package that provides a collection of methods for intrinsic molecular subtyping of breast cancer. It includes subtyping methods for nearest centroid-based subtyping (NC-based) and single sample predictor (SSP-based), along with tools for integrating clinical data and visualizing results. 
Encoding: UTF-8
Version: 0.99.0
biocViews: RNASeq, Software, GeneExpression, Classification
Authors@R: c(
    person(given = "Qiao", family = "Yang", 
	    role=c("aut", "cre"), email="[email protected]", 
  comment = c(ORCID = "0000-0002-4098-3246")) 
  )
Depends:
    R (>= 4.4.0)
Imports:
    impute (>= 1.80.0),
    magrittr (>= 2.0.3),
    dplyr (>= 1.1.0),
    data.table (>= 1.16.0),
    stringr (>= 1.5.1),
    rlang (>= 1.1.4),
    ComplexHeatmap (>= 2.22.0),
    RColorBrewer (>= 1.1-3),
    circlize (>= 0.4.16),
    bslib (>= 0.8.0),
    ggplot2 (>= 3.5.1),
    ggrepel (>= 0.9.6),
    shiny (>= 1.9.1),
    e1071 (>= 1.7-8),
    methods,
    withr
Suggests:
    knitr,
    rmarkdown
URL: https://github.com/yqkiuo/BreastSubtypeR
BugReports: https://github.com/yqkiuo/BreastSubtypeR/issues
License: GPL (>= 3)
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
LazyData: FALSE
RoxygenNote: 7.3.2

[lshep]

This package currently does not interact with common Bioconductor classes. You mention gene expression and clinical data which would likely mean your package should work with a SummarizedExperiment Object. You can also look at structures like BiocSet or GSEABase for gene sets.

Also 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.

[yqkiuo]

Hi @lshep,

Thank you so much for your comments. And I made changes to the BreastSubtypeR package as below.

• Work with a SummarizedExperiment Object.
• Provide an abstract/a motivation in the vignette.

Best,
Qiao