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Published 20 hours ago • verified publisher icon Bioconductor

SpatialDeX

Open lchengy1024 opened this issue 1 year ago • 7 comments

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

  • Repository: https://github.com/wang-lab/SpatialDeX

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.

lchengy1024 avatar May 16 '24 02:05 lchengy1024

Hi @lchengy1024

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: SpatialDeX
Type: Package
Title: What the Package Does (Title Case)
Version: 0.99.0
Authors@R: c(
    person("Xinyi", "Liu", email = "[email protected]",
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-5716-8264")))
Maintainer: Xinyi Liu <[email protected]>
Description: The rapid development of spatial transcriptomics (ST) technologies has
    enabled transcriptome-wide profiling of gene expression in tissue sections. 
    Despite the emergence of single-cell resolution platforms, most ST 
    sequencing studies still operate at the multi-cell resolution. Consequently,
    deconvolution of cell identities within the spatial spots has become 
    imperative for characterizing cell type-specific spatial organization.  
    To this end, we introduce SpatialDeX, a regression model-based method for
    estimating cell type proportions in tumor ST spots.  SpatialDeX exhibited
    comparable performance to reference-based methods and outperformed other
    reference-free methods with simulated ST data. Using experimental ST data,
    SpatialDeX demonstrated superior performance compared with both 
    reference-based and reference-free approaches. 
License: GPL-2
Encoding: UTF-8
LazyData: false
Imports:
  dplyr,
  GSVA,
  copykat
RoxygenNote: 7.3.1
Data: extdata/cyclegenes.RData extdata/DNA.hg20.RData extdata/full.anno.RData
biocViews: Spatial, Transcriptomics, Software
URL: https://github.com/wang-lab/SpatialDeX/
BugReports: https://github.com/wang-lab/SpatialDeX/issues
VignetteEngine: knitr::rmarkdown
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
Depends: 
    R (>= 2.10)

bioc-issue-bot avatar May 16 '24 02:05 bioc-issue-bot

Thanks for this submission!

Title: What the Package Does (Title Case) should not be used as the Title field in DESCRIPTION

The Import of copykat may be problematic because the package is not in CRAN or bioconductor. See the last clause of section 1.1 at https://contributions.bioconductor.org/bioconductor-package-submissions.html ... you may wish to encourage the copykat developer to contribute the package to CRAN or Bioconductor, or remove the role of copykat from your package.

vjcitn avatar May 16 '24 03:05 vjcitn

General

  • [ ] All packages must be on CRAN or Bioconductor. copykay does not appear to fit this criteria. You will not be able to list it as a dependency or utilize it in the package until it is on CRAN or Bioconductor

License

  • [ ] You include GPL-3 but list GPL-2 in the DESCRIPTION. Please update to 3 in the description

inst

  • [ ] Please include an inst/script directory that documents how the data in extdata was generated. Include relevant source and licensing information. This can be text, psuedo code, or code.

lshep avatar May 20 '24 14:05 lshep

May we expect any updates soon?

lshep avatar Jun 24 '24 16:06 lshep

Hello,

Sorry for the delay. We are working on encouraging the copykat developer to contribute the package to CRAN or Bioconductor. However it may unlikely to happen. Is there alternative option to solve this issue? Thank you.

Best, Xinyi

On Tue, Jun 25, 2024 at 12:52 AM lshep @.***> wrote:

May we expect any updates soon?

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3422#issuecomment-2187006274, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7M2WVPLQMIIFGOFSNGPXN3ZJBFGHAVCNFSM6AAAAABHZI5ZPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBXGAYDMMRXGQ . You are receiving this because you were mentioned.Message ID: @.***>

lchengy1024 avatar Jun 25 '24 13:06 lchengy1024

Unfortunately all packages must be on CRAN or Bioconductor. If copykat is unwilling to submit you could check on their licensing and include the functionality directly in your package, only if proper credit is given to original authors. Otherwise it must be removed from the package to be included in Bioconductor.

lshep avatar Jun 25 '24 13:06 lshep

Thank you for your advice. We will check the license.

On Tue, Jun 25, 2024 at 9:40 PM lshep @.***> wrote:

Unfortunately all packages must be on CRAN or Bioconductor. If copykat is unwilling to submit you could check on their licensing and include the functionality directly in your package, only if proper credit is given to original authors. Otherwise it must be removed from the package to be included in Bioconductor.

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3422#issuecomment-2188997653, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7M2WVJK4EWGOV5RILVJKEDZJFXORAVCNFSM6AAAAABHZI5ZPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBYHE4TONRVGM . You are receiving this because you were mentioned.Message ID: @.***>

lchengy1024 avatar Jun 25 '24 13:06 lchengy1024

Has there been any progress on this?

lshep avatar Aug 05 '24 14:08 lshep

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.

bioc-issue-bot avatar Aug 12 '24 12:08 bioc-issue-bot