Are G1/S transition cells not labeled in cyclone?

[giovanegt]

Hi all,
Thank you for this awesome tool. It is really useful.
I am running cyclone on my scRNA seq data. I noticed the I have cells on G1, S or G2/M but not G1/S transition, and I expected to have several cells on G1/S transition. Can't cyclone label cells on G1/S transition?
What happens to the G1/S transitioning cells within cyclone classifier? Are they labeled as S-phase cells?
Can you separate G2-phase cells from M-phase cells with cyclone?

Appreciate the feedback.

Best,

[antoscial]

Hello, Thanks for your email and your interest in the tool. Cyclone will only classify cells in G1, S or G2M, since these were the labels included in the training dataset - so you can’t distinguish G2- from M-phase cells (unless you have a separate dataset for training). To identify cells that might be at G1/S transition, you would have to look at the individual scores calculated by cyclone: cells at G1/S transition will have a G1 score approximately equal to the S score (and much greater than the G2M score). All the best, Antonio

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On 17. Feb 2021, at 21:56, GT ***@***.***> wrote: Hi all, Thank you for this awesome tool. It is really useful. I am running cyclone on my scRNA seq data. I noticed the I have cells on G1, S or G2/M but not G1/S transition, and I expected to have several cells on G1/S transition. Can't cyclone label cells on G1/S transition? What happens to the G1/S transitioning cells within cyclone classifier? Are they labeled as S-phase cells? Can you separate G2-phase cells from M-phase cells with cyclone? Appreciate the feedback. Best, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4OKXKM4DGR4DHYH2R32DDS7QURFANCNFSM4XZCBTOQ>.

[giovanegt]

Thanks for the clarification.Appreciate it.