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dpeerlab / spectra

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
MIT License
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use_cell_types not implemented in Spectra_gpu #32

Open ccruizm opened 9 months ago

ccruizm commented 9 months ago

Good day!

I want to use spectra for each main group of cells (myeloid, lymphoid, etc) in my tumor data. In that case, I want to set use_cell_types=False, but this option is not implemented for GPU. When do you think it will become available?

Thanks in advance!

ccruizm commented 9 months ago

This was working in the previous version (before the name change to scSpectra). I want to use this new version since it seems there are some new implementations since the last time I tested it :)

Why does the new version of the package not support use_cell_types=False when using GPU? Would it be an option to assign all cells to a cell type and run it as if they are labeled?

wallet-maker commented 8 months ago

Hi Cristian, sorry for the delayed response. We are still working on the GPU version. I think your workaround should do. To be safe I recommend you only use global gene sets if you set all cells to one cell type.