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omnideconv / SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
http://omnideconv.org/SimBu/
GNU General Public License v3.0
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only use high confidence cells #14

Closed grst closed 2 years ago

grst commented 2 years ago

Not sure in which repo this fits best as it makes sense essentially everywhere where signatures are generated. In particular also relevant for @constantin-zackl's future signature curation efforts.

The idea is to distinguish between cells of which we are (relatively) confident the annotation is correct, and less confident ones.

A solution could be a graph-based appraoch as discussed in https://github.com/omnideconv/k-mer-deconvolution/issues/2

FFinotello commented 2 years ago

I think it is relevant for both the simulator and training of second-generation methods. We could maybe implement a general module for preprocessing?

grst commented 2 years ago

Good idea. In that case it should probably go to omnideconv?

FFinotello commented 2 years ago

Good idea. In that case it should probably go to omnideconv?

Do you mean omnideconv\omnideconv? I would say so, unless we do not envision something like omnideconv\preprocessing

grst commented 2 years ago

Do you mean omnideconv\omnideconv

yes. I don't think we need another package.