totalVI, peakVI, multiVI with scRNA-seq and scATAC-seq data

[Z_Huang]

Hi community,

I am new to scvi-tools and I went through all of the tutorials. I learned peakVI consumes scATAC-seq data for DNA analysis; totalVI consumes CITE-seq data for RNA and protein analysis.

Here is my question, multiVI consumes both scRNA-seq and scATAC-seq data. Does it mean multiVI is capable to analyze DNA, RNA, and protein at the same time?

Another question is: can scRNA-seq and scATAC-seq data be used interchangeably in the totalVI model? I know some people treat scRNA-seq and scATAC-seq data interchangeably in their models. Is that the case for totalVI?

Hope someone can clarify my questions. Thanks.

[adamgayoso]

@Z_Huang

Here is my question, multiVI consumes both scRNA-seq and scATAC-seq data. Does it mean multiVI is capable to analyze DNA, RNA, and protein at the same time?

MultiVI can currently handle ATAC + RNA. In the next few weeks it will do all three.

@Z_Huang

Another question is: can scRNA-seq and scATAC-seq data be used interchangeably in the totalVI model? I know some people treat scRNA-seq and scATAC-seq data interchangeably in their models. Is that the case for totalVI?

No, in general the models in scvi-tools are specifically designed for the noise properties of the data. Therefore, totalVI can only be used with RNA + Protein.

[crhodes]

MultiVI can currently handle ATAC + RNA. In the next few weeks it will do all three.

@adamgayoso Is there any update on this, especially documentation?

Thanks

[martinkim0]

Hi, sorry for the late reply. MultiVI currently works for ATAC + RNA + protein, but it currently expects all modalities to be in the same AnnData. We are working on adding support for MuData to make this process simpler.