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

Notebook for integration of scRNA with scATAC #9

Open

swapnilkeshari opened this issue Dec 9, 2024 · 1 comment

swapnilkeshari commented Dec 9, 2024

I wanted to analyse a multiomic data using this method. I was curious how can I do so?

Owner

jaydu1 commented Dec 11, 2024

Hi, thanks for your interest. Here is the notebook for the case study with scRNA and scATAC data we presented in the paper: Jupyter notebook.

For scATAC data, we use gene activity scores returned by Cicero (which was downloaded from Granja et al. as .rds files).
This script converts .rds objects to .h5 files that Python can read: rds_to_h5.R
Then, we simply concatenate the gene expressions and gene activity scores as a single adata:
```
adata = anndata.concat([adata_rna,adata_atac], index_unique=None)
```
with metadata concatenated accordingly.

Hope this helps with your question.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment