FunGeST

I have the same question. I am also interested in suggested parameters to run Velocyto on snRNA-seq data. Thanks a lot!

Hi, Sorry for the late reply. The probability of a specific mutation being attributed to a given signature depends on the overall signature decomposition for the sample. So if you...

Hi Jamie, Thanks for getting in touch, and I'm sorry for not getting back to you sooner. I haven't seen this issue before, even when working with sparse datasets as...

Thanks! Please note that some of the function names have now changed, see the [example script](https://github.com/FunGeST/Palimpsest/blob/master/RUNNING_PALIMPSEST_EXAMPLE/Palimpsest_Test_Script.R) for more information on this (e.g. NMF_Extraction() has replaced deconvolution_nmf()).

Hi, There are probably ways to avoid overlapping labels in R but we have not had the time to implement this in Palimpsest yet. I would suggest manually correcting the...

Hi, Please see section 5.6 of the package [vignette](https://nbviewer.jupyter.org/github/FunGeST/Palimpsest/blob/master/Files/vignette_palimpsest_2.0.pdf) and our [2017 paper](https://www.nature.com/articles/s41467-017-01358-x) for examples of how we used the origins function to study and plot the distribution of signatures...

Hi there, Thanks for getting in touch. Yes you probably should receive more clonality information than that you're right! Would you be able to provide some example data so I...

Hi, I can see that chromosomes in "CHROM" column of your cna_data object contain no "chr" prefix. This is an issue since Palimpsest uses these values to match with the...

Hi, Thanks for getting in touch, and I apologise for not getting back to you sooner. Regarding your first issue, I think it may just be caused by SBS_OSCE1 and...