satuRn

[jgilis]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/statOmics/satuRn

Confirm the following by editing each check box to '[x]'

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• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

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[bioc-issue-bot]

Hi @jgilis

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: satuRn
Type: Package
Title: Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Date: 2021-01-26
Version: 0.99.5
Authors@R: c(person("Jeroen", "Gilis", role = c("aut","cre"),
           email = "jeroen.gilis@ugent.be"),
   person("Kristoffer", "Vitting-Seerup", role = "ctb",
           email = "kristoffer.vittingseerup@bio.ku.dk"),
         person("Koen","Van den Berge", role = "ctb",
             email = "koen.vandenberge@ugent.be"),
         person("Lieven","Clement", role="ctb",
             email = "Lieven.Clement@ugent.be"))
Description: satuRn provides a higly performant and scalable framework for performing
    differential transcript usage analyses. The package consists of three main functions.
    The first function, fitDTU, fits quasi-binomial generalized linear models that model
    transcript usage in different groups of interest. The second function, testDTU, tests    
    for differential usage of transcripts between groups of interest. Finally, plotDTU  
    visualizes the usage profiles of transcripts in groups of interest.
Depends: R (>= 4.0)
Imports: locfdr,
     SummarizedExperiment,
     BiocParallel,
     limma,
     pbapply,
     ggplot2,
     boot,
     Matrix,
     stats,
     methods,
     graphics
Suggests:
    knitr,
    rmarkdown,
    testthat,
    covr,
    BiocStyle,
    AnnotationHub,
    ensembldb,
    edgeR,
    DEXSeq,
    stageR,
    DelayedArray
VignetteBuilder: knitr
Collate:'data.R' 'satuRn-framework.R' 'allGenerics.R'
        'accessors.R' 'fitDTU.R' 'testDTU.R' 'plotDTU.R'
License: Artistic-2.0
URL: https://github.com/statOmics/satuRn
BugReports: https://github.com/statOmics/satuRn/issues
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.1
biocViews:
    Regression,
    ExperimentalDesign,
    DifferentialExpression,
    GeneExpression,
    RNASeq,
    Sequencing,
    Software,
    SingleCell,
    Transcriptomics,
    MultipleComparison,
    Visualization

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/satuRn to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 3641a9a8c2300c7d3ae0887bc0a88f3d6e921c07

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/satuRn to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Kayla-Morrell]

@jgilis - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review. Overall, this is a really well put together package. Very well organized, written, and documented. I have just a few points below.

General package development

• [x] REQUIRED: There are some files that either need to be removed or moved to another location. In the 'man/' directory, the 'figures/' directory should be in the 'inst/' directory. What is the purpose of the 'dev/' directory? This is usually not something we allow in our packages. If it's not necessary it should be removed.

Vignette

• [x] REQUIRED: The installation section should demonstrate to the user how to install from Bioconductor and not from GitHub. The code should look something like the following and should include eval = FALSE.

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("satuRn")

• [x] REQUIRED: All sections of code should be exectutable, is there reason for having the sections at lines 171 and 204 as eval = FALSE?

R code

• [x] REQUIRED: Unexported object imported by a ':::' call: 'locfdr::locmle'.

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 99 lines that are > 80 characters long.

• [ ] SUGGESTION: For formatting reaosns, consider multiples of 4 spaces for line indents. There are 22 lines that are not.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: c9fd2bee47c4eb3b1cf5c8351fb4b5e94855a0e6

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/satuRn to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[jgilis]

Dear Kayla,

Thank you very much for your kind words in the previous review. This is the first time I submit to Bioconductor and even the first time I published an R package for external use. The fact that the package was immediately quite close to the desired output really is a testament to the convenience of the BiocCheck package and the extensive documentation for the submission procedure as provided by Bioconductor.

That said, I recently made a new push to accommodate your remarks. All requirements should now be met. I also worked on meeting your suggestions, reducing the number of long lines and troublesome indents. However, some troublesome indents remain (also upon running styler), in particular in the man pages created by roxygen2.

Looking forward to completing the submission procedure,

Kind regards,

Jeroen

[Kayla-Morrell]

@jgilis - Thank you for making the required changes and attempting to clear up the suggestions as well. I have looked over the changes and everything looks good. I'm more than happy to accept the package.

Best, Kayla

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/jgilis.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("satuRn"). The package 'landing page' will be created at

https://bioconductor.org/packages/satuRn

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.