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AntonioDeFalco / SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
https://www.nature.com/articles/s41467-023-36790-9
GNU General Public License v3.0
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Did the count_mtx include stromal cells #28

Closed cystone closed 1 year ago

cystone commented 2 years ago

As the question. When we input the count_mtx. Do we have to extract the epithelial cells before the SCEVAN process, or do we input the whole count_mtx including immune cells endothelium and fibroblasts. Thanks for your excellent scRNAseq tools.

AntonioDeFalco commented 2 years ago

Hi @cystone, Thanks for your interest in our tool. Yes you have to input the whole countmtx including immune cells endothelium etc.. and SCEVAN classify normal and tumor cells and then perform the entire analysis. In the case of already known normal cells, you can pass the vector of their names as parameter norm_cells_.

I hope this is clear.