Skip to content

review omics data assignment for cell line data #343

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
sgosline opened this issue Mar 27, 2025 · 0 comments
Closed

review omics data assignment for cell line data #343

sgosline opened this issue Mar 27, 2025 · 0 comments
Assignees
@jjacobson95

Comments

@sgosline
Copy link
Member

sgosline commented Mar 27, 2025 •
edited
Loading

GDSC data is missing a large number of transcriptomics data.

how many sanger cell lines have transcriptomics? how many broad cell lines have transcriptomics?

For each dataset, how many cell lines are MISSING transcriptomic data in the Sanger dataset (but mislabled) OR the broad data? We need to review our approach to selecting cell lines before moving forward.
sgosline added a commit that referenced this issue Mar 31, 2025
@sgosline
fix for #343
71f624c 
Here we separate out the omics data early on in the pipeline to ensure better assignment.
jjacobson95 added a commit that referenced this issue Apr 14, 2025
@jjacobson95
Merge pull request #345 from PNNL-CompBio/sanger_data_fix
beeb65d 
fix for #343
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@jjacobson95 jjacobson95

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@sgosline @jjacobson95