@johanneskoester.bsky.social
Professor for Bioinformatics and Computational Oncology University of Duisburg-Essen Author of Snakemake, founder of Bioconda
@fxwiegand.bsky.socialReposted by @johanneskoester.bsky.socialThe plot is highly customizable by choosing marks, aggregation, color and size mappings and can be directly exported to publication ready SVG files. We also support exporting the specs back into a datavzrd view for easy reproducibilty and more tweaking.
@fxwiegand.bsky.socialReposted by @johanneskoester.bsky.socialOur tool #datavzrd has just received a new release adding on the fly scatter plot creation for any two columns of your dataset. @johanneskoester.bsky.social
@johanneskoester.bsky.socialIn general, I am worried about three things at least. (i) the reinvent-the-wheel-instead-of-contribute syndrome will become even more abundant (can be even seen in opus‘ response, not saying that it will happen in your case of course), (ii) the danger of deskilling, (iii) the carbon footprint.
@johanneskoester.bsky.socialSo, I found the first „bug“ in the response. What else might be there :-)…
@johanneskoester.bsky.socialShouldn‘t it be Myers :-)?
@brent-p.bsky.socialReposted by @johanneskoester.bsky.socialWe continue to improve bedder. It does interval intersections on VCF, BED, etc and lets users write python expressions on the intersection to drive output (including modifying VCF INFO fields).
It will also use an index where possible to avoid extra parsing.
Give it a go: github.com/quinlan-lab/...
@pola.rsReposted by @johanneskoester.bsky.socialWe just released Polars 2.0.
It removed many of our legacy decisions makes the streaming engine our default and promotes SQL to a first class citizen within Polars.
pola.rs/posts/releas...
@johanneskoester.bsky.socialRegistration for the #SnakemakeHackathon2027 is open now. This time, it will be at the Paul-Scherrer-Institute in Switzerland. Details and registration: indico.cern.ch/e/snakemake2...
Please spread the word!
@johanneskoester.bsky.socialI have just release #rust-bio 4.1.0 containing various bug fixes (e.g. for gap extensions in pairHMMs) and support for IUPAC codes in our homopolymer aware pair HMM flavor (homopolypairHMM).
@fxwiegand.bsky.socialReposted by @johanneskoester.bsky.socialOur portable alignment viewer #alignoth now supports working with remote BAM files similar to samtools. Simply update to version 1.11 via cargo, conda or pixi and you are good to go.
#bioinformatics #genomics #rustlang @johanneskoester.bsky.social
@fxwiegand.bsky.socialReposted by @johanneskoester.bsky.social#datavzrd config files now get autocomplete and inline validation right in your editor thanks to schemastore. Just name the file *.datavzrd.yaml and Zed, VS Code and most other IDEs should pick up the schema automatically.
@johanneskoester.bsky.social
