SigMA
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parklab
Mutational signature analysis for low statistics SNV data
Hi, I'd like to run SigMA on a novel gene panel, have I understood correctly that it can be done by following the example in test_determine_cutoff.R and in the Wiki...
To there: Hi. I am using your software to define sig3 from panel data.I have some questions about the result: 1. This package is designed to filter sig3 from panel...
Hi, I have a query about SigMA. Is it possible to run without organ specified (because I intend to run on experimental samples)? Any help is appreciated. Best regards Salome
Dear Park lab team, Thanks for sharing SigMA - amazing tool. I have a quick question: I would like to do mutational signature deconvolution of IMPACT samples with various tumor...
Hi, I am trying to apply it to panel data, but found the sum of all the exp_sigs is not equal to the number of total_snvs. Some samples have the...
Hi! We are interested in training a new model for a different gene panel; the [guide](https://github.com/parklab/SigMA/wiki/Optimize) helped a lot. We want to detect other signatures beyond Sig3. I have read...
Hi, I'm interested in the number of WGS samples needed if I want to make my own data simulations for a custom panel. I noticed that in matrices_96dim.rda the number...
Hi, I ran the example file test.R which uses vcf file. Here there is a different output format other than lite_format. After running the following code, run(genome_file, data = "msk",...
Hi! I am following the [tune example](https://github.com/parklab/SigMA/blob/master/examples/test_tune_example.R). We first provide our dataset to run SigMA and tune it based on our data. How big should our dataset be? The tcga_mc3_brca.maf...
Hello, I'm trying to use SigMA to detect Signature 3 in mesothelioma samples. I followed the steps in the Wiki, but got somewhat confusing results. It reported no presence of...
