Jayaram Kancherla

a year ago we (+@realAaronLun) announced Kana (kanaverse.org/kana/), to perform #singlecell analysis in the browser powered by #webassembly. This week we released version 3 to support multi-modal data analysis, gene set enrichment and exploration of pre-analyzed results (1/n)

Seamlessly access R/Bioconductor annotations in Python! The new "txdb" package lets you load standard TxDb SQLite databases and work with genomic features as native #BiocPy `GenomicRanges` objects. Try it: `pip install txdb` docs: github.com/BiocPy/txdb

forgot to tag: @realAaronLun

If you're building Python pipelines for genomics, check out GenomicRanges. For feature requests or feedback, reach out to us on GitHub! Try it: `pip install genomicranges` Contribute: github.com/BiocPy/Genomic… #BiocPy

The GenomicRanges (github.com/BiocPy/Genomic…) package for Python got a major speed boost (v0.7.0+) thanks to Aaron’s blazing-fast C++ nclist interval indexing! #Bioinformatics #Genomics #Bioconductor

If this generation is Gen Alpha, I say we call the next one Gen AI—because they'll probably ask ChatGPT than reddit for advice.

Join our ML for Genomics group working directly with me on spatial biology. careers.gene.com/us/en/job/2024…

Powerful use of the RNA-targeting Csm complex! We've now extended the crisprVerse to make CRISPR-Csm gRNA design easy: github.com/crisprVerse/Tu…

@passle_ @PaoloDiTommaso next step is replace to-regex-range with a one liner...

lol, removing is-number from this package saves 440gb weekly github.com/micromatch/to-…

@dagarfield @nomad421 the mice community disagrees ;)

@nomad421 We briefly considered AI buttons on actual mice, but the market research was not great....

I mean, we are at the point in the AI bubble where companies are putting dedicated AI buttons on computer mice. There's only one way for this hype train to go from here...

@nomad421 @vsbuffalo also congrats 👏

@nomad421 @vsbuffalo no Python downstream?

TFW you want to talk to your amazing collaborator about what looks like great news, but they don't check commons as obsessively as you and so they don't know yet 🤣. I'm really excited about what we're going to build!

Really nice writeup on the hugely impressive MetaGraph work by @gxr, @akkah21, @m_karasikov, @HarunMustafa416 (& others whose handles I don't know) in @ScienceMagazine: science.org/content/articl…. Some comments by @ZaminIqbal, Lesley Hoyles and myself! Congrats @m_karasikov & team!

@AstraKernel javascript?

I feel one programming community has a superiority complex It is not Rust, not Go, not Java... Don't ask me which one. You will know when you see them

@nomad421 Can non-rust folks join as well? #askingforafriend 🙂

If you've joined our #rustseq GitHub organization, please check out the issues on the "planning-and-discussions" repo for a link to join our Zulip channel! If you're interested in joining the #rustseq organization but aren't a part of it yet, please reach out!

Check out our work today at #ICLR2024. We insert a concept bottleneck layer into generative models, which allows us to interpret, control, and debug them. This is a first step towards interpretable generative modeling! @juliusadml @hcorrada @stephenrra @kchonyc

@vsbuffalo @isugif I wonder how this compares to tiledb - docs.tiledb.com/main/integrati…

I think there is a huge benefit to standardizing a chunked on-disk binary typed arrays (e.g. Zarr) to store VCF data. Then, build bioinformatics and population genomics software on top of this format. bio2zarr is alpha but I'm very excited: github.com/sgkit-dev/bio2…

@madhurarrao ask an LLM to summarize them all...

@strnr Thank you for sharing these threads, these have been super helpful 👍

What I’m reading this week in microbial genomics, data/metadata standards, misc bioinformatics tools, … 🧬🖥️🧵

How to pick a problem. Today in @CellCellPress. 1/53 cell.com/cell/fulltext/…