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CostaLab / scopen

scOpen: single-cell open chromatin analysis via NMF modelling
GNU General Public License v3.0
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Can I run scopen with TF-IDF matrix? #18

Closed bitcometz closed 1 year ago

bitcometz commented 2 years ago

Hello, Thanks for this great software.

Could I run scOpen with TF-IDF as inputs. For more specific, my ATAC-seq peak counts have been transformed with TF-IDF using the default log(TF) * log(IDF) output (chromatin accessibility) and stored as h5 format.

Thanks !!!

lzj1769 commented 1 year ago

Hi,

The command line of scOpen does not support running it on transformed matrix, unfortunately.

However, you can use the NMF function provided by scopen to perform dimensionality reduction. In this case, you might need to implement a few functions to access the data in h5 format and call the function in sOpen.

Best, Zhijian