QRscore

[Fanding-Zhou]

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• Repository: https://github.com/songlab-cal/QRscore

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[bioc-issue-bot]

Hi @Fanding-Zhou

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: QRscore
Title: Quantile Rank Score
Version: 0.99.0
Date: 2024-12-01
Authors@R: c(
    person("Fanding", "Zhou", email = "[email protected]", role = c("cre","aut"),
    comment = c(ORCID = "0000-0003-1306-740X")),
    person("Alan", "Aw", email = "[email protected]", role = c("aut"), 
    comment = c(ORCID = "0000-0001-9455-7878")), 
    person("Dan", "Erdmann-Pham", email = "[email protected]", role = "aut"),
    person("Jonathan", "Fischer", email = "[email protected]", role = "aut", 
    comment = c(ORCID = "0000-0002-1165-9930")),
    person("Xurui", "Chen", email = "[email protected]", role = "ctb")
    )
Description: In genomics, differential analysis enables the discovery of groups of genes implicating important biological processes such as cell differentiation and aging. Non-parametric tests of differential gene expression usually detect shifts in centrality (such as mean or median), and therefore suffer from diminished power against alternative hypotheses characterized by shifts in spread (such as variance). This package provides a flexible family of non-parametric two-sample tests and K-sample tests, which is based on theoretical work around non-parametric tests, spacing statistics and local asymptotic normality (Erdmann-Pham et al., 2022+ [arXiv:2008.06664v2]; Erdmann-Pham, 2023+ [arXiv:2209.14235v2]).  
License: GPL (>= 3)
Depends: MASS, pscl, arrangements, hitandrun, assertthat, dplyr, BiocParallel
Suggests: 
    devtools,
    DESeq2,
    knitr,
    rmarkdown
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2023-07-10 07:50:30 UTC; fandingzhou
VignetteBuilder: knitr
biocViews: StatisticalMethod, DifferentialExpression

[lshep]

Could you please expand your vignette to have more descriptions on what each section of code is doing.

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

[Fanding-Zhou]

Hi! Thanks a lot for the comments. I've expanded the vignette to have more descriptions and included an intro section.