scRNAseq + scTCRseq

[aarebeca]

Hi,

Wondering if is it possible to use BPCells for a dataset that contains scRNAseq and scTCRseq?

Thank you for this great package!

Best,

Rebeca

[bnprks]

Hi @aarebeca, thanks for your question! You can definitely use BPCells to analyze the scRNA-seq portion of your data and combine those results for plotting with any values or metadata you might get out of a scTCR-seq analysis.

BPCells doesn't contain any scTCR-seq specific functionality, so you will likely need to do at least some of the TCR alignment, similarity detection etc. with outside tools. BPCells main data types are matrices and genomic fragment sets (e.g. from scATAC-seq), though some of the plotting functions like plot_embedding() let you pass in any vector of values to plot, which could come from an outside scTCR analysis tool.

What kinds of analysis tasks would you be looking to do with scTCR-seq + BPCells? If you think some of the TCR data might fit well in a matrix, I can give pointers on BPCells functions that might be useful for the calculations you are trying to perform.

-Ben