Skip to content
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

Which model should I use for a cell typing task #185

Closed
abearab opened this issue Apr 3, 2023 · 2 comments
Closed

Which model should I use for a cell typing task #185

abearab opened this issue Apr 3, 2023 · 2 comments

Comments

@abearab
Copy link

abearab commented Apr 3, 2023

I have a question regarding the use of your tools, and it would be more convenient to discuss it here. I am currently analyzing a single cell dataset obtained from a mouse neuronal region, with three different treatment conditions and several replicates per condition. I already used scvi which has been helpful in my experience. However, we faced difficulties in identifying neuronal subtypes. Despite the availability of a rich reference for this region (see here), I am considering utilizing your tools to integrate our data with the existing dataset to facilitate cell typing. Could you please advise me on which model to select? Thank you in advance for your assistance.
@abearab
Copy link
Author

abearab commented Apr 3, 2023

SCANVI, right?
https://scarchest.readthedocs.io/en/latest/scanvi_surgery_pipeline.html

@Koncopd
Copy link
Member

Koncopd commented Apr 4, 2023

Yes, this model.

@Koncopd Koncopd closed this as completed Apr 6, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@Koncopd @abearab