AntonioDeFalco / SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
https://www.nature.com/articles/s41467-023-36790-9
GNU General Public License v3.0
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Is there a maximum of subclones? #93

Open augjensen opened 1 year ago

augjensen commented 1 year ago

Thank you for this SCEVAN tool which I use a lot at the moment,

I am analysing merged datasets to investigate patient-specificity among CNV subclones. However, using a merged dataset of 24 donors, generating 12 subclones, there was an error at the end of the analysis pipeline. How should I interpret this error? Is there a maximum to the amount of subclones that can be analyzed (9)?

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Thanks in advance!

DGladish commented 10 months ago

I am also curious about this. I am analyzing two samples from the same patient (taken at different times). With these datasets merged in datasets from 2 healthy donors (P1 + H1/H2, P2 + H1/H2, P1+P2+H1/H2), and specified these as the healthy cells. When I do these 3 runs, the number of subclones produce from the runs on the individual datasets are more than the number of subclones from the runs on the merged dataset.

P1+H1/H2: 5 subclones P2+H1/H2: 5 subclones P1+P2+H1/H2: 6 subclones

naila53 commented 3 weeks ago

@augjensen wondering if you managed to figure out this issue?I'm facing the same error when merging samples however it works fine when running the pipeline on individual samples.

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