Get overall classification per cell (diploid vs aneuploid)

[ccruizm]

Good day,

Thanks for developing this great tool! I used it in my scATAC, but I would like to know whether there is a systematic way to classify cells as diploid or aneuploid so that I can add that information directly to the metadata of each cell.

Thanks in advance for your help!

[thek71]

Hi,

we are currently working on the subject.
It will probably be included in a newer version of the tool.

[ccruizm]

Thanks @thek71 . Do you think will be available soon?

[thek71]

Hi @ccruizm , we are still working on it. I will keep you informed.

Best,
Katia

[ccruizm]

Thanks for the update! Looking forward to trying in the next release :)

[ccruizm]

Hi @thek71! Do you know when the next version will be available? I am eager to try it :)

Thanks!

[thek71]

Hi @ccruizm, we are having some problems with the implementation. Basically we cannot find a good dataset with groundtruth to test correctly. We still hope to be able to incorporate such a function, but so far it has been proven tricky.
If you have any suggestions please feel free to share them.

Best,
Katia

[Krithika-Bhuvan]

Hi Katia - just saw this post. If you are looking for a good dataset to use as ground truth, I suggest a colon cancer dataset, and a brain cancer dataset. Both of those have well known copy number alterations. 4q deletion on colon cancer is very well known in stage II patients (PMC3149118). In gliomas, Human IDH mutant have 1p/19q co-deletions (PMC7367867). Hope this can help narrow down your search for a good ground truth dataset.