Palimpsest

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Dear Palimpsest team. When reading through your Introduction to Palimpsest, I can see that you recommend nrun = 20 for large data set for SBS/DBS/indel mutational signatures analysis. Is this...

AndreVidas

Visualising the results of mutation origin

1

Hello I was able to run origin function but I don't know how to visualise that or any possible plot (if already produced by function) goes where This is the...

beginner984

error in DBS & ID denovo signatures extract

1

Hello, I got some errors using the above command. Hope you can any help. DBS_denovo_sigs NMF::nmf - 10/10 fit(s) threw an error. # Error(s) thrown: - run #1: non-conformable arrays...

shiguangyini

Calculating ntot for your software

1

Hello I am trying to figure out how I can get the `ntot` required for clonality analysis I have `ploidy`, `purity`, `major` and `minor allele copy number` I googled for...

MaryGoAround

Providing input file for software

2

Sorry Is there any function in your software which extracts require fields like CHR, POST, REF, ALT, VAF, ... from a .vcf file (SNP or INDEL or SV) ? Because...

MaryGoAround

kant

What does this error mean

4

Hello I am getting this error ``` > str(SV) 'data.frame': 3904 obs. of 10 variables: $ Sample : chr "CHC018T" "CHC018T" "CHC018T" "CHC018T" ... $ Type : Factor w/ 4...

beginner984

Same mutation in two different signatures

4

Hi, I have been running Palimpsest on mutations in whole genome and same mutations but falling in specific regions of the genome. I observed that in these two different runs,...

rahulk87

Few number of clonal and sub-clonal variants

3

Hello By `393472 SNPs` for `17 samples`, after running your software I am getting `600 clonal variants and 83 sub-clonal` the rest are NA Do you think something is going...

beginner984

Signatures Contributing to Driver Genes

2

I keep throwing the same error every time I try to plot the drivers vs signatures plot: > matprob sig.cols for(i in 1:nrow(matprob)){ + g

mkinnaman