SigProfilerMatrixGenerator
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AlexandrovLab
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file)....
Hi, I would like to use the `generateCNVMatrix` function on copy-number files generated by [PURPLE](https://github.com/hartwigmedical/hmftools/tree/master/purple#output). When I look through: - The example file `all.breast.ascat.summary.sample.tsv`, - the code of `generateCNVMatrix`, it...
recently I download the copy number segment from https://cancer.sanger.ac.uk/cell_lines/download. But the data comes from the file type PICNIC which you did not provide. So I would like to know if...
I just updated the SigProfiler packages, and the update installed the latest SciPy 1.12.0. When running SigProfilerMatrixGenerator, it eventually crashed because the SciPy stats function binom_test, which was previously deprecated...
- Add support for VCF inputs for SV matrix generation - Update README
https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/blob/8360cbe3c0e3e0392a9addba9639ceb18a2dd7f6/SigProfilerMatrixGenerator/scripts/convert_input_to_simple_files.py#L1306 this line should be `start = str(int(start) - 1)` without the `-=`
https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/blob/f945199230a4fc0671d90a7873b079930a84d227/SigProfilerMatrixGenerator/scripts/convert_input_to_simple_files.py#L332C10-L332C10 Hello, why are the hyphens added to `ref` and `mut` when the other functions don't do similar actions? This breaks downstream because they are added again in MutationMatrixGenerator.py (lines...
Hello, Thank you for developing SigProfiler tools. I noticed an error with the new version of pandas (2.0.0) : `AttributeError: 'DataFrame' object has no attribute 'append'` I was able to...
I got this error when I run this function in R. Do you know why it comes from and how I can address it? Running SigProfilerMatrixGeneratorR... Starting matrix generation for...
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SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file)....