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pinellolab / dictys

Context specific and dynamic gene regulatory network reconstruction and analysis
GNU Affero General Public License v3.0
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How to use separate scRNA-seq and scATAC-seq data to Create dynamic GRN ? #36

Closed thinkingpeach-z closed 7 months ago

thinkingpeach-z commented 8 months ago

Dear Lingfei,

Thank you for developing such a wonderful package. I noticed that in the tutorial, it mentioned that the Human blood data was used to construct a dynamic GNR based on separate scRNA-seq and scATAC-seq. I also have separate data. How can I use Dictys to construct a dynamic GNR?

lingfeiwang commented 8 months ago

Dear thinkingpeach-z,

Thank you for your interest. You need to integrate them into the same low dimensions. Then you can infer a trajectory in this low dimension with both data types together, in the same way as the dynamic GRN for SHARE-seq or 10x multiome in other tutorials. You also need to set JOINT to 0 in the configuration step. Other steps are the same with the tutorial. Please let us know here if you have any followup questions.

github-actions[bot] commented 7 months ago

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