Closed HElias01 closed 1 year ago
@ribogod
Thank you for your feedback. Unfortunately I did not make script for ArchR/SeaCell. The key element for the input data is co-accessibility score data between scATAC-seq peaks. Please take a look at this notebook, section #1. https://morris-lab.github.io/CellOracle.documentation/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/02_preprocess_peak_data.html#1.-Load-scATAC-peak-data-and-peak-connection-data-made-with-Cicero
If you can prepare data in this format, you can use another package.
I am currently very busy and have not had much time to respond to requests for a CellOracle analysis. I expect this busyness to continue for a while yet, so I can't get time to answer requests right now. However, we are planning a major update to CellOracle itself and the tutorials. We will work on this in the near future.
Kenji
If we are working with ArchR instead of Cicero, what are the key elements to prepare input data of base GRN construction?