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.

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

Implement pathway analysis using decoupler #6

Open
Tracked by #3
nictru opened this issue Jun 13, 2024 · 3 comments
Open
Tracked by #3

Implement pathway analysis using decoupler #6

nictru opened this issue Jun 13, 2024 · 3 comments
Labels
enhancement New feature or request

Comments

@nictru
Copy link
Collaborator

nictru commented Jun 13, 2024

https://decoupler-py.readthedocs.io/en/latest/index.html

@nictru nictru added the enhancement New feature or request label Jun 13, 2024
@nictru nictru added this to the Stable transcriptomics milestone Jun 13, 2024
@gabora
Copy link

gabora commented Jun 13, 2024

Hello @nictru,
there is a decoupler nf-core module for bulk analysis (https://nf-co.re/modules/decoupler_decoupler by @Nic-Nic and @vicpaton ) which could probably be a good starting point for this new feature. It handles multiple samples given in a matrix, so if you provide the single cell data as a matrix then it can return the enrichment scores per cells. Reach out to us if we can help,
best
Attila

@nictru
Copy link
Collaborator Author

nictru commented Jun 13, 2024

Thank you very much! Will get back to you :)

@grst
Copy link
Member

grst commented Jun 13, 2024

I would even argue that bulk analysis is what you want most of the time, see also this decoupler tutorial:
https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

3 participants