PlasmodiumgenomeData Submission for ExperimentHub

[ocheab]

The PlasmodiumgenomeData package provides curated genome datasets for various Plasmodium species, supporting bioinformatics and genomic analyses. This package includes preprocessed genomic data in .rds format, which is ideal for integration with R-based workflows. The data is intended for researchers studying Plasmodium genetics and related fields.

GitHub Repository
The package source code is hosted on GitHub:
[PlasmodiumgenomeData Repository](https://github.com/ocheab/PlasmodiumgenomeData)

Adherence to Bioconductor Guidelines

• The package adheres to Bioconductor’s guidelines.
• It includes a valid metadata.csv file located in inst/extdata/.
• The data files are appropriately managed using Git LFS for large file handling.

Request

We kindly request the inclusion of PlasmodiumgenomeData in ExperimentHub. Please let us know if there are any additional requirements or modifications needed for submission.

Thank you for your time and consideration.

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

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

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

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

• 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.

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

• 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.

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

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[lshep]

A few follow up questions/comments:

1. Bioconductor does not support Git LFS as stated in the contributions guidelines.
2. This being the case may we recommend hosting the data on a service like zenodo or another secure, public location like a S3 bucket or data lake. We can then add the data to the experimenthub for easy download/caching/search ability within Bioconductor. We will close this issue as it also had an issue doing prechecks from changing the submission template. You can continue to ask questions about the experimenthub/data submission here or by contacting [email protected].
3. When you re-submit please keep the template starter changing the link to your repository only and please do not make it a markdown link format, just the url: ie:

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

- Repository: https://github.com/ocheab/PlasmodiumgenomeData

Confirm the following by editing each check box to '[x]'
<rest of template>

4. Also before re-submission, Please read Bioconductor guidelines. Despite this being a data package you should still have a vignette that describes the data and once accessible for download from the hubs probably code to show how to find the resources.
5. I cannot load your data so I'm not able to preview it but curious at what format and information is provided in the rda file. Depending on the type of data you should look into standard Bioconductor classes for formatting if not done so already.

Cheers,