visualize the feature importance scores - Seqweaver

[goutha...@gmail.com]

Hi All,

This is a question not directly related to Selene.

I am using the DIS from deepsea (chromatin data) and seqweaver (RBP data) from the whole genome deep learning analysis paper. https://www.nature.com/articles/s41588-019-0420-0

I ran the two models on a set of variants and I found the DIS impact scores to be very useful. I am also interested to look at individual TFs or RBPs that are effected by my variants, to highlight some examples in publication. I am wondering, if there is a way to visualize  the feature importance scores from the seqweaver in-silico mutagenesis using selene or other frameworks ?

Thanks,

Goutham A

[chen.ka...@gmail.com]

Hi Goutham,

You can run & visualize in silico mutagenesis for SeqWeaver through HumanBase: https://hb.flatironinstitute.org/deepsea/?preset=ism

You can also generate some out-of-the-box visualizations for ISM in Selene: http://selene.flatironinstitute.org/interpret.html

(There's a notebook showing how to do this but it might be outdated - https://github.com/FunctionLab/selene/blob/master/manuscript/case1/3_visualize_ism_outputs.ipynb)

Hope that's helpful!

Kathy

[goutha...@gmail.com]

Thanks Kathy for pointing to these useful resources.