Repository navigation
Gene list: add vfb-scRNAseq's FBgn list; give every expressed gene a class - #45
Merged
Merged
Conversation
…class scRNAseq is moving from the old FlyBase/SCEA loads (vfb-scRNAseq-ontology) to vfb-scRNAseq. Its expression/FBgn_list.txt is added to the gene list (the old list kept until the old loads are retired), and every gene in the list now gets a Gene class: 31 current genes vfb-scRNAseq expresses (e.g. non-coding CR genes) are missing from fbgn_fbtr_fbpp, so their expression edges would point at genes VFB does not have. Co-Authored-By: Claude Opus 5.5 <[email protected]>
Contributor
Author
|
Blocked for now: VirtualFlyBrain/vfb-scRNAseq is private, so the anonymous |
Contributor
Author
|
Unblocked: VirtualFlyBrain/vfb-scRNAseq is now public, and https://raw.githubusercontent.com/VirtualFlyBrain/vfb-scRNAseq/main/expression/FBgn_list.txt returns 200. It now includes the Ing-Simmons fix (VirtualFlyBrain/vfb-scRNAseq#101): genes only, 15,516 FBgns. |
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
scRNAseq data in VFB is moving from the old FlyBase/SCEA loads (vfb-scRNAseq-ontology) to vfb-scRNAseq, which publishes
expression/FBgn_list.txt(VirtualFlyBrain/vfb-scRNAseq#100, merged).Changes
process_FBgn.pyadds the listed genes to those fromfbgn_fbtr_fbpp). 31 current genes that vfb-scRNAseq expresses are not Gene classes in VFB production: mostly non-codingCR…genes, plusCG42778andpog. Without a class, theirexpressesedges would point at genes VFB doesn't have.Not run locally: the build needs the manually downloaded FlyBase files described in the Makefile.
🤖 Generated with Claude Code