About only tumor cell (cluster)

[soralsr]

Hi @AntonioDeFalco, thanks for this amazing package.

I met problems, when I used SCEVAN to identify heterogeneity in tumor cluster ( only tumor cell ).

PipelineCNA results detected the normal cells in tumor cell cluster, when I applied it. (I used only tumor cell)

Can't I just detect the tumor cell (not contain normal cell) using SCEVAN?

Expecting your reply.
Thank you

[AntonioDeFalco]

Hi @soralsr,
For the inference of the copy number from scRNA data SCEVAN, like other methods, requires the use of a reference of normal cells to infer the copy number, which is why SCEVAN assumes that in the matrix of a tumour sample there is the presence of some tumour microenviroment cells to be used as a reference. Therefore, I do not advise using only tumour cells for heterogeneity analysis; it is possible to use the synthetic reference generated from the data with SCEVAN, but I recommend adding normal cells to the matrix to obtain a more reliable copy number analysis.

Thanks. Regards