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Hello,
Thanks for a great tool! I have been using it to randomize the position of mutations in samples while controlling for mutational signatures. However, I have noticed that I am not getting the…
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Anywhere in fgbio we need to access FASTA for reference genomes or similar we end up using HTSJDK's `ReferenceSequenceFile` and related classes (`ReferenceSequenceFileFactory`, `ReferenceSequence`). …
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Does SigProfilerAssignment work for targeted panels such as TSO500 and FMI CDx? I guess not?
If it works, is there anything special to keep in mind when applying SigProfilerAssignment to targeted P…
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Hi, I hope I'm not missing anything, but in the paper that came out earlier this year, it was mentioned that there were two steps to extracting the COSMIC signatures- SigProfilerExtractor and SigProfi…
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Hello,
I try to use SigProfilerAssignment on ~70 samples but I am stuck with an error.
I call the function Analyze.cosmic_fit this way:
```
Analyze.cosmic_fit(samples="../outputs/mutational_sign…
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Hi, Shixiang
Thanks for developing this great tool! I have 2 questions.
1)
I used maftools to merge a couple of maf files and loaded it to sigminer, and followed by the workflow as below:
#----…
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Keeping track of timings for the sessions on the workshop that ran 11th Dec 2023. To help with timetable in the future.
**day 1**
- 09:40 - 09:50 Welcome (hugo)
- 09:50 - 10:15 Know your bug (A…
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hi processor @mdbarnesUCSD
I change my code and use the given parameters
The cpu usage is still very low.
When it gets the "making matries for INDELs", the cpu usage is too slow.
It costs too mu…
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## Description
Hello! I have run the `Analyze.decompose_fit` function from SigProfilerAssignment to decompose several SBS96 _de novo_ signatures using a signatures database. There were no problems du…
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Hello,
following the installation instructions for PCGR 2.0.0 via conda, I am encountering an issue when installing pcgrr. This is the exact command I am using:
```
#install PCGR
PCGR_VERSION=…