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morris-lab / CellOracle

This is the alpha version of the CellOracle package
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Query: Prepare base GRN construction with ArchR #144

Closed HElias01 closed 1 year ago

HElias01 commented 1 year ago

If we are working with ArchR instead of Cicero, what are the key elements to prepare input data of base GRN construction?

KenjiKamimoto-ac commented 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