Added notebook to fetch Pharos class information for genes in Agora #158
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
BWMac
approved these changes
Nov 20, 2024
|
I cleared the outputs. No other code changes in latest commit. |
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Outdated suggestions cannot be applied.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.
This PR addresses AG-1563 by fetching Pharos classes for all genes in Agora data sets (except druggability).
The results are merged with the UniProt mapping file to get Ensembl IDs corresponding to each gene, and the final result has been uploaded to Synapse here. There are ~2000 genes that exist in Pharos that are not in our data sets, so these get removed during the merge.
A human-readable version of the notebook is here.