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as per @songt need to add the clonal column into the portal file (data_mutations_extended.txt) for helix filters
It comes from the same facets file as ASCN.TOTAL_COPY_NUMBER
So clonality from th…
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I've tried to follow the use guide for inputting cnvkit segmentation files, but keep running into the following error:
```
Error in if (is.na(posterior) || posterior < 0.5) flag lapply -> lapply …
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Hi,
I successfully performed TCR repertoire analysis on my single cell dataset.
Now I would like to perform some statistics and visualize them based only on one of the two chains (for example calcu…
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Hi there!
In summary, Im estimating CCF values and I've noticed that some mutations which I would have expected to be sub clonal (CCF
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Hi,
I hope you can help me to understand the output from battenberg.
In the output of the call subclones part of the pipline a "segmentation file" is produced. This file has the clonal / subclonal…
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Hi,
Thanks for the very interesting manuscript accompanying this code. I really enjoyed reading it.
I have a question related to the functional use of the tool using long-read sequencing (nanopo…
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Hi there,
I am trying to run palimpsest https://github.com/FunGeST/Palimpsest.
Their SV requirement is
```
Sample: Sample identifier. Any alphanumeric string.
Type: Type of structural variant…
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Dear Prof
Thanks for your contribution to maftools R package. When I calculated the MATH scores of all the melanoma samples from TCGA database, it kept processing up to 7 days without output…
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Hi,
I started running my superfreq.R script with all the metadata and 2 reference normals. I see this Variants DB in my directory but why does this fail to load?
`>>>>Rscript` test_superfreq_run…
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I met the same error. I guess the bug may be inside the complement() function from get_features() function. When both length(miss_Pat) >0 and length(miss_drv) > 0.
For my data, M is a 8 x 14 tibble…