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jaydu1 / scVAEIT

Variational autoencoder for single-cell integration and transfer learning.
MIT License
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Integration of CITE-seq and scMultiome #10

Open hoseok-lee opened 5 days ago

hoseok-lee commented 5 days ago

Hi,

I'm currently looking to use scVAEIT to integrate two different datasets, CITE-seq (containing scRNA-seq and protein abundance) and scMultiome (containing scRNA-seq and scATAC-seq). They have mutually exclusive cells, but I was hoping to use the scRNA-seq modality present in both datasets to integrate all three modalities (scRNA-seq, protein abundance, chromatin-accessibility).

As all of the tutorials showcase integration for cases where there are equal or more datasets being integrated than modalities (for example, the trimodality merge contains DOGMA-seq, ASAP-seq, and CITE-seq), I was wondering how I could set up the configuration of the model for the case where there are more modalities than datasets. For example, I'm not sure how to approach how to set-up the batches and id_datasets configuration, in addition to the masks matrix.

Any help is appreciated! Thank you in advance :)

jaydu1 commented 4 days ago

Hi, thanks for your interest. I have added a Notebook that uses toy data examples to illustrate how to prepare data input for scVAEIT. It contains utility functions to concatenate multiple datasets with multiple modalities. Let me know if you have further questions.