Implement a web interface

[julistanley]

It would be really convenient to have a GUI to upload wig files, run peak calling, view the Z-score distribution and see how changing the z-score cutoff affects peaks

I think I can do this with Shiny and IGVjs. Dash might also work?

[miraep8]

Lets do IGVjs? Since you already have some stuff working with that right? You might remember I was writing something for this from scratch, but using a pre-existing interface like IGV is in my opinion 100% the way to go!

[julistanley]

There's some additional functionality that might be helpful that I meant to include in this issue, basically:

1. Upload .wig files, .fasta genome, and .gff features
2. Click a button to run peak calling on those .wig files
3. Visualize histogram of Z-scores
4. Have a slider to pick Z-score cutoff
5. igvJS window updates with both the .wig files and an additional track with peaks, along with a button to download tracks.

I think 1-4 can be a Shiny app, since those can also load & run python libraries via reticulate.

For 5: Shiny technically supports custom js, but practically it would take some legwork to get igvJS implemented there¹. Luckily, Paul Shannon did the legwork for us: https://github.com/paul-shannon/igvShiny, I was just waiting for him to implement custom genome annotations, which it looks like he just finished

Footnotes

1. Sidenote: You can see here a test of igvJS with our data--it works well, except that merged tracks don't quite autoscale correctly yet--individual tracks scale just fine, but obv merged tracks are pretty necessary for 5' and 3' Rend files. The maintainer is working on fixing that, see igvjs #1473 and igvjs #1506. ↩

[miraep8]

Overall I think it sounds like a great idea! Want to take it on since you have an idea of where you want to go with it/have worked with IGVjs before? [Edit: nevermind - I just saw you already assigned yourself!]

[miraep8]

So I guess there has been some progress on this currently with your Shiny app and the interface on rendseq.org. Feel like we could potentially plug in some of these functionality on what you have already built?