mspms

[baynec2]

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• Repository: https://github.com/baynec2/mspms

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[bioc-issue-bot]

Hi @baynec2

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: mspms
Type: Package
Title: Analysis tools for use with MSP-MS
Version: 0.99.0
Authors@R: person("Charlie", "Bayne", email = "baynec2@gmail.com",
    role = c("aut", "cre"))
Description: This package provides functions for the analysis of data generated 
    by the multiplex substrate profiling by mass spectrometry for proteases 
    (MSP-MS) method.Data exported from upstream proteomics software is accepted 
    as input and subsequently normalized, outlier removed, and imputed. 
    Tools for statistical analysis, visualization, and interpretation of 
    the data are provided.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
Depends: 
    R (>= 4.1.0)
biocViews: Proteomics, MassSpectrometry
Imports: 
    dplyr (>= 1.1.4),
    magrittr (>= 2.0.3),
    MASS (>= 7.3.60.0.1),
    NormalyzerDE (>= 1.19.7),
    outliers (>= 0.15),
    purrr (>= 1.0.2),
    stats (>= 4.1.1),
    tidyr (>= 1.3.1),
    truncnorm (>= 1.0.9),
    utils (>= 4.1.1),
    ggplot2 (>= 3.5.0),
    ggseqlogo (>= 0.2),
    heatmaply (>= 1.5.0),
    readr (>= 1.1.5),
    readxl (>= 1.4.3),
    rstatix (>= 0.7.2),
    tibble (>= 3.2.1),
    SummarizedExperiment (>= 1.24.0),
    rlang (>= 1.1.3),
    forcats (>= 1.0.0),
    ggpubr (>= 0.6.0),
    rmarkdown (>= 2.26),
    DT (>= 0.33)
Suggests: 
    knitr,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
URL: https://github.com/baynec2/mspms
BugReports: https://github.com/baynec2/mspms/issues
VignetteBuilder: knitr

[lshep]

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.

Please do not hard code paths in vignettes/examples/tests. For example

"../tests/testdata/protein-peptides-lfq.csv"

Data should be in a inst/extdata directory and data should be
well documented on source, licensing, and how it was generated either with a file in inst/script that can be text, pseudo code or code but detail how a user could procure or created the files in inst/extadata. Then retrieve the path with system.file().

[baynec2]

Just edited as you suggested and pushed changes!