spent some time last weekend getting higlass to play nicely inside @marimo.io

molab.marimo.io/notebooks/nb...

From there, it's the normal resgen interface except that the current project is the current directory.

If this sounds a lot like the erstwhile higlass-manage functionality, it is because it's modeled after it. Just with more sophisticated directory and metadata handling.

To get started, install resgen-python, start an instance in any directory, create a user, sync data and open browser:

pip install resgen-python
resgen manage start .
resgen manage create-user
resgen manage sync-datasets

Alright, it's still very much a work in progress, but you can now run resgen locally to view data that's on your machine without uploading to resgen.io.

docs.resgen.io/local/runnin...

Small new feature: the ability to collapse tracks to free up space. Thanks to Johan Gibcus for the suggestion!

Did you know oxbow powers resgen? We use it to load bam and bigwig tiles. Great library!

Comparison of the resgen.io home page and the similarly styled docs page

Small but satisfying update over the weekend to (mostly) sync the styling between the main page and docs page:

Pssst 🤫... you can also try this live with @genomeinabottle.bsky.social data here:

resgen.io/paper-data/Z...

A screenshot of the new resgen.io home page showing recent projects and recent views.

New year, new home page! Trying to make it easier to get to recently viewed projects and views. Access via the "home" button on the top menu bar when logged in.

Also added a small news feed to highlight recent updates you may or may not have noticed.

Happy new year!!

Forgot about BLAT. That may work. Thanks!

I guess BLAST does this but its indexes are pretty hefty.

I wonder what it would take to search for a single sequence that may vary from 100 - 10k nt in length across hundreds of vertebrate genomes in less than a second 🤔.

Surely the index needs to be loaded into memory. Minimap2 seems promising or an online version of BWA?

And of course, a live link for anybody wishing to try this out themselves:

resgen.io/l/?d=YrhQaXb...

Pileup support is shaping up to be both performant and beautiful thanks to the Rust powered Oxbow package:

github.com/abdenlab/oxb...

Big shout out to @nvictus.bsky.social and @manzt.sh for implementing key features like buffering and file-like pointer support!

Not terribly mobile friendly either 🤔. Will have to work on that.

Got a version of paired-end read pileups out. The aesthetics are nice but the layout algorithm needs some work. Still not quite ready for prime time.

Nevertheless, here's a link to try it out with data from a Gorilla genome from Yoo et al. 2024 (Eichler lab).

resgen.io/paper-data/Y...

😍😍

Less noticeable are back end updates to the UI framework. This brings it up to date and eliminates a large amount of technical debt.

Large changes invariable introduce some instability. Please excuse the inconvenience and reach out if you encounter any issues.

Also, some minor UI cleanups. Notably, the entire dataset can be dragged onto the browser to view.

Big update over the weekend: datasets can now be organized into folders!

Also, the default ordering for projects is by the last time they were opened. Soon to come is an option to select how they are ordered.

If this existed, one could mirror an entire directory tree in a resgen project, just like github.

Thinking of making the tilesets list support nesting, like a file browser 🤔. Tags and descriptions wouldn't change.