resgen_io (@resgen_io) profile picture

resgen_io

@resgen_io

A repository of genome-indexed information and next-gen genome browser located at https://xitter.cf/t.co/51RpO5Mh5J. Built w/@higlass_io.

Joined January 2020
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Docs for how to run this locally: docs.resgen.io/local/running…
Peter Kerpedjiev (@pkerpedjiev) profile picturePeter Kerpedjiev@pkerpedjievFeb 14
Or you could use higlass / resgen, which has had this functionality since 2000, only requires BAM files and can be run locally right now. See for yourself with this @GenomeInABottle dataset. resgen.io/paper-data/Zook%20…
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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/running…
Image from resgen_io (@resgen_io)
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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
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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.
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Did you know oxbow powers resgen? We use it to load tiles for bigwig and bam files. Great library!
Nezar Abdennur (@nv1ctus) profile pictureNezar Abdennur@nv1ctus7 Jul 2025
Proud to announce the latest release of 🧬#Oxbow🏹, with new features to make NGS data analysis more powerful, efficient, and "composable". Learn more at: oxbow.readthedocs.io/
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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 Gorilla data from Yoo et al. 2024 (@EichlerLab). resgen.io/paper-data/Yoo%202…
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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.
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Also, some minor UI cleanups. Notably, the entire dataset can be dragged onto the browser to view.
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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.
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Turns out this requires updating a bunch of outdated UI components and that is taking forever🤦‍♂️
resgen_io (@resgen_io) profile pictureresgen_io@resgen_io25 Oct 2024
Thinking of making the tilesets list support nesting, like a file browser 🤔. Tags and descriptions wouldn't change.
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Thinking of making the tilesets list support nesting, like a file browser 🤔. Tags and descriptions wouldn't change.
Image from resgen_io (@resgen_io)
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If this existed, one could mirror an entire directory tree in a resgen project, just like github.
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Hot tip: If you're having resgen / higlass performance issues on Chrome on Mac OS X, try entering "about://flags" in the url bar and setting "Choose ANGLE graphics backend" to "OpenGL".
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We've been serverless for a couple months now. It's been growing pains but performance and scalability is improving. There's a new caching layer that should improve responsiveness for the most frequently used tilesets.
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Finally switched resgen.io backend to serverless. This enables much greater scalability. Please excuse and report any hiccups you may encounter in the next few days.
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For the record, hardware acceleration is indeed enabled in Chrome:
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Thanks to @nv1ctus for pointing out the poor performance in Chrome! We'll work to improve it.
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PSA: For reasons unkown, resgen seems to perform much better in Firefox than in Chrome. Below is a screencap in Firefox and in the replies is a screencap from Chrome. The difference is astonishing.
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Screencap of sluggish Chrome behavior. It wasn't always this way. Chrome used to perform better than Firefox. It's unclear when the tables turned.
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Modified github.com/pkerpedjiev/s3sql… to take a file-like object and read beddb (gene annotation) files. Next up BAM files using github.com/abdenlab/oxbow. Slowly getting closer and closer to a scalable and serverless resgen.io 🤞
GitHub - pkerpedjiev/s3sqlite: Query SQLite files in S3 using s3fs

GitHub - pkerpedjiev/s3sqlite: Query SQLite files in S3 using s3fs

Query SQLite files in S3 using s3fs. Contribute to pkerpedjiev/s3sqlite development by creating an account on GitHub.

github.com
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Big thanks to @nv1ctus for getting file-like support for BAM files implemented in github.com/abdenlab/oxbow 🙏 Works like a charm 👌
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