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)....
It is not named what I expect based on the progress message that I saw. ``` Saved aggregate SV32 plot to /dski/dario/HeadNeck/structuralVariants/forSigProfiler/OSCC_RS32_counts_aggregated.pdf $ ls forSigProfiler/ # Not OSCC_RS32_counts_aggregated.pdf. OSCC.SV32.annotated.tsv OSCC.SV32.matrix.tsv...
I just installed and ran SigProfilerMatrixGenerator 1.2.26, and it fails with an error that binomtest does not take a parameter _x_. The points in MutationMatrixGenerator.py all use binomtest(x=. According to...
Hi, I would like to run de novo extraction for copy number from a cancer cohort that contains both male and female. Should the copy number segments of chrX and...
Dear all, SPT uses the pyrimidine strand column of the mutation after SPMG call for replication strand asymmetry analyses. However, the pyrimidine strand is 0 for some doublets and indels...
Dear all, Normally, SigProfilerSimulator simulates as gender='female' by default. But I want to check whether there are mutations on chrY and if yes, I want to run SigProfilerSimulator simulates as...
Previously `trans` and `untrans` have been appending another DataFrame, either `a` or `b`. Fixed #133 by applying a simple fix: using `concat` instead of `append`.
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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)....