masyahook
commented
1 month ago @Flu09 thank you for showing interest in using scGRN!
How to use scGRN when I have different conditions ? Is there a notebook to follow to compare between them?
This notebook contains the code where you can compare samples. For example, on the picture below under group I label samples which are controls / moderate and severe cases - this is the metadata that you need to create. You can create a similar dataframe and try to run the notebook, I'm here to help. Please expect some errors because the code was tested only on COVID dataset.
Prior to running the notebook, you need to run the network_inference pipeline (I assume you already ran single cell processing with Seurat or similar). Depending on the type of network you are inferring, you can also do community analysis.
do I keep them in the same object?
All GRNs are stored as physical objects on disc either as gpickle networkx objects or adjacency matrices. When you run analysis functions, the function loads the data and provides the visualizations.
If you provide more concrete information what you are trying to achieve, maybe I can point you to exact code that you can use. What type of network you are using - TF <-> target, or gene <-> gene? As you used aucell, I assume you want to focus on pathway analysis? You can have a look at this notebook in this case.
Hello, I have different conditions and their controls and I am interested in using scGRN but I am not sure how to start. I am familiar with pyscenic and computing aucell and RSS. How to use scGRN when I have different conditions ? do I keep them in the same object? or different ones (I have the 2 auc matrix for each condition (healthy included in it) Is there a notebook to follow to compare between them?