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colomemaria / epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data
GNU General Public License v3.0
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Get overall classification per cell (diploid vs aneuploid) #8

Open ccruizm opened 1 year ago

ccruizm commented 1 year ago

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 commented 12 months ago

Hi,

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 It will probably be included in a newer version of the tool.

ccruizm commented 8 months ago

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

thek71 commented 8 months ago

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

Best, Katia

ccruizm commented 8 months ago

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

ccruizm commented 7 months ago

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

Thanks!

thek71 commented 7 months ago

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 commented 3 months ago

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.