SigProfilerAssignment
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AlexandrovLab
Assignment of known mutational signatures to individual samples and individual somatic mutations
* Use SigProfilerPlottings custom_text_upper and custom_text_middle to include the stability and mutation count to the de novo signature plots for SBS4608.
I recently ran SigProfiler on some TCGA data and got samples enriched for SBS signatures with values like "SBS288", "SBS384", "SBS1536", "SBS4608", and "SBS6144." What signatures are these referring to?...
Hi there, Just wondering if you could set this dir as somewhere else like a "temp working directory"? https://github.com/AlexandrovLab/SigProfilerAssignment/blob/7fef91c5e1c898ccad482e4a3a783bcef53366ec/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py#L48 The current setting works fine when you have "write permission" to...
Pressing Ctrl-C once realising incorrect file name is specified does nothing. ``` Assigning COSMIC sigs or Signature Database ...... 1/15 [7%] in 0s (~0s, 18339.6/s) ^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C ``` It would be...
When using `cosmic_fit` to assign mutational signatures to my samples, I identified SBS1, SBS5, and SBS19. I then extracted these three signatures to refit using `denovo_fit`. However, I noticed differences...
README file doesn't explain difference to SigProfilerSingleSample. Also, it seems SigProfilerAssignment can't do structural variants.
Hello! I am trying to use `decompose_fit()` to decompose a set of denovo signatures into a catalogue of reference signatures. I am passing in the catalogue using the `signature_database` parameter....
Hi, I get this error when using the software. This is my input data and database. my code is Analyze.cosmic_fit('path/my_data.txt', 'SBS96', input_type="matrix", context_type="96", exome=False, genome_build="GRCh38", signature_database ='path/hg38_cosmic_V34_exome.txt') [my_data.txt](https://github.com/user-attachments/files/18288426/my_data.txt) input data...
Hi there, Hope you're doing well! I had a quick question about using SigProfilerAssignment. When I input SBS288 or SBS1536-dimensional context and signature matrices for the signatures and samples parameters,...
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Assignment of known mutational signatures to individual samples and individual somatic mutations