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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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Simulation inputs and options #4

Closed FFinotello closed 2 years ago

FFinotello commented 3 years ago

Hello!

I was thinking about the input of the simulator, which could be an annotated single-cell dataset plus a text file with the desired fractions per cell type.

However, users might be not skilled enough to design a proper simulation. So we could provide some options/modules to compute the cell fractions (and then derive the corresponding pseudo-bulk dataset) in an automated way, following the scenarios that @grst already implemented in the immunedeconv paper (e.g. spillover analysis). I think the scripts for such simulations are readily available, right!?

Cheers, Francesca

FFinotello commented 3 years ago

Maybe inspiring for (additional) simulation scenarios: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02290-6

grst commented 2 years ago

superceded by https://github.com/omnideconv/benchmark/issues/1 and #7