Update ORA and GSEA report #266
Merged
Conversation
This file contains 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
|
Thanks for taking care of this! |
LMBradford
added a commit
that referenced
this pull request
Dec 16, 2024
This reverts commit 586f9c9.
Merged
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Report was failing because clusterProfiler functions don't properly download KEGG data. Syed previously changed it to use a file downloaded from KEGG medicus, but that solution wasn't great. Here, I use the KEGGREST package to connect to KEGG and download the necessary information, depending on the organism used in the study. This is more flexible.
Still to do: rearrange and simplify the report.