-
I'm looking at some exposures I have calculated but I'm a bit confused as to how I should interpret the y-axis. I got 5 signatures and for none of them I have any exposure values larger than 10%, so t…
-
#### What analysis module should be updated and why?
The [mutational-signatures analysis module](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/dev/analyses/mutational-signatu…
-
> Hi,
> when to use this parameter, collapse_to_SBS96=True?
_Originally posted by @me-nobody in https://github.com/AlexandrovLab/SigProfilerAssignment/issues/78#issuecomment-1666535662_
…
-
I ran SigProfilerAssignment for 396 HCC samples across a mutational matrix constructed using SigProfilerMatrixGenerator from PCAWG vcfs (lifted over to GRCh38) or vcfs from our own in house mutation …
-
Hello.
I want to extract mutational signatures from a dataset, however, I am facing some problems regarding the 'trinucleotideMatrix' function. I already tried to indicate in ref_genome as 'BSgenome…
-
I would like to try out the algorithm but there is no information what the input format should be. VCF file format as input would be very much preferred for this type of algorithm. "standard CSV forma…
-
Hi @dami82,
More than an issue is a question regarding the getCosmicSignatures() function. I noticed when it is used, it pulls the 30 COSMIC SBS signatures, however, when you download directly fro…
-
Hello, I am using sigprofilerExtractor version 1.1.21 and plotting version 1.3.14. I encountered the following error and would like to know the cause. Thank you.
```
KeyError …
-
https://www.nature.com/articles/s43018-020-0050-6
This study contains the following data types:
- Mutations
- Copy number alterations
- Structural variants
- Gene expression
- Mutational signa…
-
Dear Team,
Sorry to trouble you.I have a few questions to ask.
I got the segments files from "SEQUENZA", Below is an example:
sample chromosome start.pos end.pos Bf N.BAF sd.BAF depth.ratio N.r…