Mouse RefCDS for dNdScv package

Question

[isd1989]

Hi all

I am trying to run the dNdScv package to identify mutations that are under positive selection. The dataset I am working with is sequencing data from mouse tumours using a targeted gene panel.

The default for the package is using human data. Does anyone have a RefCDS object already for mouse (mus musculus) that I can use to apply the algorithm to my data?

Here is the page for the package: dNdScv

Thank you!

Answer 1

[Inigo Martincorena]

Hello

Thank you for your interest in dNdScv. You can find a number of RefCDS for other species, including mouse, in this link: https://github.com/im3sanger/dndscv_data/tree/master/data

You can also use this tutorial to generate your own RefCDS for any species or transcript dataset of interest.

Best, Inigo

[isd1989]

Thank you Inigo, and thank you for all your work with this package!

Best wishes.