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When calling CNV.segment, get the following error:
"Erreur dans if (min(weights)
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### Description of the bug
When the user adds a cnv correction with the config file, the pipeline takes ages and then fails
[count_table.count.txt](https://github.com/user-attachments/files/16331863…
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Hi,
I'm having issues trying to run SigProfiler for CNV data using custom CNV calls. We have an in-house pipeline for CNV calls that is similar to the ASCAT approach, tailored to our WGS data. I t…
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Hello! I've been trying to use your software, but I only ever see global CNV changes - no hint of single cell changes.
I've tried changing the windows size between 1e5, 5e5, and 1e6, the minFrags …
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Dear UCSCXena developers,
While querying the tcga_surv_get function for the prognostic value of the CNV feature of gene signatures in the latest versions (UCSCXenaShiny version 2.1.0 and UCSCXenaSh…
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If the `cnv_region` contains multiple genes, the CNV heatmap rows will be ordered by the gene label rather than their genomic position. This can make it a bit confusing to try to understand the struct…
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Currently missing CNV HMM data due to high coverage variance is rendered in white in the CNV heatmap. Normal copy number of 2 is also rendered as white. This can be confusing and allow mistaken interp…
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Hi,
I am using copykat to calculate CNV on a cancer sample, and results showed that not only cancer cells, but also there were a lot of macrophages with CNV.
Could macrophages have CNV in cancer sa…
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Hi team
I realise that Spectre may struggle on CN calling in adaptive sampling due to stochastic read depth variation - have a sample that has undergone adaptive LR of BRCA. There is a clear DUP on…
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Dear developers,
Thank you very much for this advanced tool. I have a number of questions on modelling of CNVs on Tapestri data (thousands of cells and 400 amplicons):
1. I am interested in both…