RamEx

[qibebt-bioinfo]

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• Repository: https://github.com/qibebt-bioinfo/RamEx

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[bioc-issue-bot]

Hi @qibebt-bioinfo

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: RamEx
Type: Package
Title: Ramanome Explorer is a R package for comprehensive and efficient analysis and comparison of ramanomes.
Version: 0.99.0
Authors@R: 
    c(
        person("Yanmei", "Zhang", role = c("aut"), comment = "Co-Author"),
        person("Gongchao", "Jing", email = "[email protected]", role = c("aut", "cre"))
    )
Description: By providing simple-to-use modules for computational tasks that otherwise would require substantial programming experience and algorithmic skills, RamEx should greatly facilitate the computational mining of ramanomes.More complete information about how to use RamEx can be found in the [github](https://github.com/qibebt-bioinfo/RamEx), but here you'll find a brief overview of the function and examples to mining of ramanomes:
License: GPL
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (>= 3.0), RColorBrewer, Rcpp, circlize
Imports:
   MASS, MLmetrics, Matrix, NMF, parallel, Rtsne, cowplot, data.table, dbscan, disprofas, doParallel, dplyr, e1071, fastICA, foreach, ggforce, ggplot2, ggthemes, grDevices, graphics, hyperSpec, ica, igraph, mdatools, methods, pheatmap, irlba, prospectr, purrr, randomForest, rlist, scales, stats, stringr, utils, uwot, vegan, Cairo, Hmisc, proxy, reshape2, ggtext, mclust, RcppAnnoy, ade4, magrittr, corr2D
Suggests:
    testthat,knitr, RcppParallel, Rcpp, gpuR
biocViews: Visualization, Clustering, Software
Config/testthat/edition: 3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-11

[qibebt-bioinfo]

Hi, following up to make sure this doesn't get lost.

Best,
Qibebt

[lshep]

We normally process packages within 1-2 weeks. I will likely be looking at this today or next week mon/tue.

[lshep]

Please also provide an inst/scripts directory that describes how the data
in inst/extdata was generated. It can be code, pseudo-code, or text but
should minimally list any source or licensing information.

Please have a package level man page so when a naive user does ?RamEx there is
information on how to get started with the package.

It would be good to increase testing coverage.

The vignette is currently not rendering properly. Please see when you install
and do vignette("RamEx")

The vignette should be expanded. It is very minimal. Currently on quick glance,
I cannot understand how I would generate a RamEx_data object to be used in your
shown functions.

Is this to be solely used with raw data from instrumentation? Is there a way to integrate with common Bioconductor classes

[qibebt-bioinfo]

@lshep
Dear lshep,
Thank you for taking the time to review the RamEx package, and I truly appreciate the feedback you provided. I have made the following modifications and updates based on your suggestions:

1. Added the RamEx-package.Rd file to implement the ??RamEx functionality;
2. Added the RamEx_data.Rd file to describe the data;
3. Increased testing coverage in testthat-main-function.R;
4. Expanded the vignette in the RamEx.Rmd file.
   Thank you very much for your work!