(inactive) SPADE submission

[thecailab]

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

• Repository: https://github.com/thecailab/SPADE

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 @thecailab

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: SPADE
Type: Package
Title: Spatially Expressed Pattern Investication Method With Spatial Transcriptomics Data
Version: 0.99.0
Date: 2024-01-20
Author: Fei Qin, Feifei Xiao, Guoshuai Cai 
Maintainer: Fei Qin <fqin@email.sc.edu>
Description: We developed SPADE, a spatial pattern investigation method, to identify spatially expressed genes within groups and between groups using spatial transcriptomics data.
License: GPL-3
LazyData: TRUE
Depends: 
    R (>= 4.0),
    stats,
    SKAT
Imports: CompQuadForm, limma
URL: https://github.com/thecailab/SPADE
RoxygenNote: 7.3.1
Encoding: UTF-8
Language: en-GB
Suggests: 
    rmarkdown
biocViews: SingleCellData, SpatialData

[lshep]

Please see contribution guidelines especially Bioconductor specific requirements. This package currently does not meet Bioconductor requirements as there is no executable vignette and should likely be inter-operating with common classes like SummarizedExperiment or SpatialExperiment.

[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.