cutleraging

ShowCategory does not work in compareCluster

1

Hi Guangchuang, I would like to only plot a subset of results from compareCluster. ``` c

What do the Z-scores of EnformerScoreVariantsNormalized() represent? Is this the relative change in the signal over 200KB centered on the variant? When I find a large Z-score and then try...

Does the enformer model support insertion and deletion variants?

``` > multik DiagMultiKPlot(multik$k, multik$consensus) Error in if (all(lineseg.df[lineseg.df$p1 == which.k | lineseg.df$p2 == : missing value where TRUE/FALSE needed ``` Any help with this?

Lower mutation number in simulation than observed

5

Hello, Thanks for a great tool! I have been using it to randomize the position of mutations in samples while controlling for mutational signatures. However, I have noticed that I...

Chromosome based error

1

Hello, I am running your tool using: ``` sigSim.SigProfilerSimulator(name, \ vcf_dir, \ "GRCh37", \ contexts=["96", "ID"], \ exome=None, \ simulations=1000, \ updating=False, \ bed_file=bed, \ overlap=False, \ gender='female', \ chrom_based=True,...

Phophopeptide quantification

1

Hello, Thanks for the great package. I have a phosphopeptide enrichment dataset. I am wondering how I can convert the diann_output.tsv to a table of phosphosites and their associated intensities....

Single cell somatic mutations

1

### Description of feature Hello, thanks for the great work with this pipeline. I would like to try to use this pipeline to call somatic mutations in single cell rna-seq...

Down-sampling spectra

3

I would like to down-sample spectra in order to know if I am close to reaching saturation of proteins identified in a sample. First I would like to know if...

slice-PASEF

1

I am testing out the 1F slice-PASEF method from your preprint and have the following questions... 1. I am wondering what the best practices are to run this in the...