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Related to PR https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1265/
The path to the fitted mutational signatures file currently used to build the supplementary tables needs to be updated fro…
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Hi, I think I found a bug in build_catalogues.
In the 5th column of the input:
-1 should equal transcribed strand
1 should equal untranscribed strand
However, build_catalogues only puts a muta…
gevro updated
2 years ago
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Dear developers,
I have been using SigProfilerExtractor to extract mutational signatures for a number of VCF files. For two of those files, no ID signatures were produced and the script exited with…
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Hi,
We use SigProfiler in our cancer genome pipeline, on some sample decomposition verbose mode produce this output:
```
################ Sample 1 ####…
natir updated
2 years ago
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I am filing this issue to replace #636 with more detailed steps required for completing the de novo mutational signatures analysis and to surface some discussion on #799 (or other, already merged PRs)…
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Dear developers,
I apologise for probably a simple question, but I was unable to find an answer in the Manual.
I have a dataset of skin cancers and want:
1.Extract de novo signatures
2.Get optim…
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Hi,
How to applied two-step signature extraction strategy with SignatureAnalyzer for hyper-mutated samples? Two-step signature extraction strategy was applied to PCAWG study in R scripts.
How t…
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**trinucleotideMatrix Does not run properly and session shut down itself**
Hi,
While running mutational signatures, I substracted a maf file preparing for computing TNM matrix thru "trinucleotideMat…
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Dear Kevin,
Would you be able to provide any additional guidance on preparing the opportunity matrix from a non-human genome for use in the convert_signatures() function? I would like to prepare an…
kmegq updated
2 years ago
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Dear @kgori ,
I am a PhD student in Bioinformatics, and I benchmarked your software package sigfit with other software packages using my in-house generated dataset. I found your package was the thi…