Referring packages in Bioc style #813
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ial_abundance.qmd
…into referring-packages
TuomasBorman
requested changes
Sep 22, 2025
|
Will do! Just note that I haven't gone through all the chapters yet, I started this PR so I could get to fixing potential issues already instead of waiting for all chapters to be done. I will notify you when all chapters are done! |
TuomasBorman
approved these changes
Sep 23, 2025
|
It is not yet ready, will probably be at the end of the week. I will inform you when it is! |
|
Cool! No worries, take your time! |
|
I have now finished all chapters! I want to point out that in resources.qmd (commit 1ee07f3) I also added the setup chunk in the beginning of the file since it was missing, and it was necessary for the BiocStyle to work. |
TuomasBorman
approved these changes
Sep 26, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
From Issue 798.
I changed all R package references to the Bioc style so it adds links automatically. I will do this to all the chapters in the OMA book.
I will also fix other small issues / faults that arise when fixing package referencing, e.g. making sure line width is still within 80 characters.