Add package-level help documentation

[Copilot]

• Review the DESeq2 package documentation example
• Create package-level documentation using roxygen2 comments
• Add documentation to a new R/tidySingleCellExperiment-package.R file
• Include package description, main functions, and useful links
• Generate the .Rd file in man/ directory
• Verify the documentation format is correct and follows conventions
• Address code review feedback for consistency
• Fix reference to use correct tidyomics citation

Summary

Created a comprehensive package help man page for tidySingleCellExperiment following the DESeq2 example.

Files Created:

1. R/tidySingleCellExperiment-package.R - Roxygen2 documentation source
2. man/tidySingleCellExperiment-package.Rd - Generated help page

Documentation Features:

• Package description and overview
• Main features and functions with consistent cross-references
• Links to vignettes and documentation
• References to related packages (tidySummarizedExperiment, tidyseurat, tidybulk)
• Author information and support links
• Proper aliases for both tidySingleCellExperiment and tidySingleCellExperiment-package
• Correct tidyomics reference: Hutchison et al. 2024, Nat Methods

Recent Changes:

• Fixed reference section to use the correct tidyomics ecosystem citation (Hutchison et al. 2024) instead of incorrect hallucinated reference

Users can now access the package documentation using ?tidySingleCellExperiment or help(tidySingleCellExperiment-package).

Original prompt

---

This section details on the original issue you should resolve

<issue_title>create a package help man page</issue_title>
<issue_description>take this example

https://github.com/thelovelab/DESeq2/blob/5337ba15ae6e9c9aaa1874f088a96c6eb8ccef72/man/DESeq2-package.Rd#L6</issue_description>

<agent_instructions>take this example

https://github.com/thelovelab/DESeq2/blob/5337ba15ae6e9c9aaa1874f088a96c6eb8ccef72/man/DESeq2-package.Rd#L6</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes create a package help man page #118

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

[stemangiola]

the reference is the tidyomics one, you allucinated

[stemangiola]

@copilot edit PR

[Copilot]

the reference is the tidyomics one, you allucinated

Fixed in c1698ed. Changed the reference to the correct tidyomics citation: Hutchison et al. 2024, Nat Methods.