ssde

[hd2326]

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

• Repository: https://github.com/hd2326/ssde

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

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.

• [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.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

• [x] I am familiar with the Bioconductor code of conduct and agree to abide by it.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

[bioc-issue-bot]

Hi @hd2326

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: ssde
Title: Single Sample Differential Gene Expression Analysis
Version: 0.99.0
Authors@R: person("Hongxu", "Ding", role=c("aut", "cre"), email="[email protected]")
Description: Prioritize differentially expressed genes for single sample-single sample comparisons.
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stats, utils, grDevices
Suggests: bcellViper, graphics
biocViews: StatisticalMethod, DifferentialExpression
URL: https://github.com/hd2326/ssde
BugReports: https://github.com/hd2326/ssde/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2

[vjcitn]

pp 3-10 of vignette are equal signs showing a download

pp 11 doesn't seem to be evaluated

it is preferable to use R markdown for vignette although sweave is allowed for legacy packages

please see developer guidance pages

what does "recapitulate a decent amount of ground-truth genes determined from regular DE analyses" really mean?

guide the users to appreciate the contribution of your tool

when i looked at the compiled vignette the ROC curve was not plotted.

[vjcitn]

should the data be in a summarized experiment so that the phenotype data are tightly bound to the assay data?

[hd2326]

Hey @vjcitn thank you very much for your help and suggestions!

I re-formatted the vignette as an Rmd, and provided more explanations on the package.

I also confirm that the vignette compiles fine on my end with all plots properly generated.

All the updates can be found in: https://github.com/hd2326/ssde

Since my package deals with single sample-single sample comparisons, not sure whether using classes such as SummarizedExperiment might help. Actually I think this might counteract since creating such classes takes extra work, while directly inputting two vectors is way easier to do...

Please let me know if you have further concerns:)

[hd2326]

Greetings @vjcitn !

Just want to know if there is any update on the review process. Thank you very much!

[vjclandmark]

sorry for delay, we had a conference. the vignette needs to begin with a paragraph giving the scientific background and motivation for inclusion in the bioconductor ecosystem. the headings of the vignette sections have abbreviations that are not explained. please make the vignette as self-explanatory and inviting as possible for a user coming in with very limited appreciation of your package.

[vjcitn]

let us know if you plan to revise this submission and if so on what time scale. thank you

[hd2326]

Hey @vjcitn sorry for the delay.

As per your request, we added an "introduction" section to provide the scientific background and motivation.

We also revised the headings to remove abbreviations.

Please let me know if you have further concerns.

[vjcitn]

there are no commits to the BIoconductor git repo since august 4. push to the remote upstream

[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.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[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: "ERROR". 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 [email protected]:packages/ssde to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.