Palimpsest
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FunGeST
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
I am having issues understanding the columns for SV inputs. It seems like `Tumor_Varcount` is the number of reads supporting the ALT in the tumor sample, and `Tumor_Depth` seems like...
Using the example script with the example Rdata gives me the following error: ``` Error in RCircos.Validate.Genomic.Data(genomic.data, "link", genomic.columns) : One or more genomic position in plot data is outside...
I followed the official guide to calculate the exposure of each de novo signatures by using the function deconvolution_fit(), but it returned with an error as following: `Error in deconvolution_fit(input_matrices...
main difference with this commit = remove `paste()` from file paths and use `file.path()` instead
Hi there, I installed Palimpsest using `devtools::install_github("FunGeST/Palimpsest")` I loaded my mutation file and formatted it accordingly. I ran annotate_VCF: ``` vcf head(maf_formatted) Sample CHROM POS REF ALT Tumor_Varcount Tumor_Depth Normal_Depth...
Dear Palimpsest developer, First of all, thank you very much for giving an opportunity to use a wonderful tool for mutational analysis. I am exciting to use this and hopefully...
Hi there, All of the data I'm using has successfully run until timing chromosomal gains. Whilst running the command I receive the following error: Command: chrom_dup_time
hi: I have a question, one driver gene is early clone mutation, but it's color isn't different from that of the signatures on the early clone, However, driber gene color...
Hello In the natural history of tumours, chromosomal arms have been intermingled and not clear like the attached plot By which argument we can make that readable please? `palimpsest_plotTumorHistories` function...
Hi, I'm analyzing SBS signatures one tumor type (extract known mutational signatures). First, I did the fitting to search signatures with real contribution (I have extracted all the cosmic signatures...
