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MarioniLab / scran

Clone of the Bioconductor repository for the scran package.
https://bioconductor.org/packages/devel/bioc/html/scran.html
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Cyclone usage #60

Closed Nusob888 closed 4 years ago

Nusob888 commented 4 years ago

Hi,

I just wanted to check whether cyclone is meant to accept a transformed/scaled gene count matrix or the raw counts? It is unclear from the documentation and there is no direct mention of this in any vignettes.

Many thanks for your help with this.

LTLA commented 4 years ago

Doesn't matter, as long as the transformation is monotonic increasing within each cell. The method is rank-based so you can give it raw counts or log-transformed values, you'll get the same result.

Nusob888 commented 4 years ago

Great thanks for clarifying @LTLA