AlexsLemonade / AlexsLemonade/refinebio
Genes Must Become First-Class Data Items
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
The [first pass](https://github.com/data-refinery/data-refinery/issues/97) of hypothetical user stories include many which require both sorting by and filtering by specific genes.
Our current output post-processors and data schema do not allow this. This ticket should track this functionality. I believe this may be something we should target for the next milestone.
I think there are three aspects to track here:
- Discovering relevant genes for a sample by parsing Salmon/SCAN output
- Adding Gene and Gene:Sample assocation tables in the database scheme
- Populating the Genes table with information from public gene databases (I assume Ensemble)
Related:
https://github.com/data-refinery/data-refinery/issues/97
https://github.com/data-refinery/data-refinery/issues/96
Contributor guide
No contributing guide indexed for this repository
Research direction
No files, tests, or entry points are named. Start by reading related issues 97 and 96, then inspect the current output post-processors and data schema. Done means tracking gene discovery from Salmon/SCAN output, adding Gene and Gene:Sample association tables, and populating gene data from a public database.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100