Tessera
Folgen

Felix Wiegand

@fxwiegand.bsky.social

👨‍💻 PhD @ Bioinformatics & Computational Oncology, UDE 🧬 Rust, data & science 🎵 Music tech & sonic tinkering 🔗 github.com/fxwiegand

18 Posts39 Follower12 Folgt
Felix Wiegand@fxwiegand.bsky.social · 4w ago

We just released a new version of #alignoth that adds support for multiple bam tracks that will get vstacked. Also many convenience features suggested by @johanneskoester.bsky.social such as automatically creating an index for bam, fasta and vcf files if they dont exit. github.com/alignoth/ali...

GitHub - alignoth/alignoth: Creating alignment plots from bam files

Creating alignment plots from bam files. Contribute to alignoth/alignoth development by creating an account on GitHub.

github.com

Felix Wiegand@fxwiegand.bsky.social · 2mo ago

On the fly column reordering is now (or at least once it has reached conda-forge) available in the latest #datavzrd version. I’ll be working on getting this to run in the paginated reports as well so it also becomes available for reports with millions of rows.

Johannes Köster@johanneskoester.bsky.social · 2mo ago

#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...

Release v4.0.0 · rust-bio/rust-bio

4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...

github.com

Jens Zentgraf@rorak.bsky.social · 8mo ago

We are excited that our paper "Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index" is now published at Bioinformatics (doi.org/10.1093/bioi...). You can find it at gitlab (gitlab.com/rahmannlab/c...) or install it via PyPI or Bioconda.

Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index

AbstractMotivation. The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many co

doi.org

Science X / Phys.org@sciencex.bsky.social · last yr.

A new open-source tool converts tabular data into interactive HTML reports without programming, enabling accessible data visualization and navigation across diverse scientific fields. doi.org/g9t2fn

New open-source tool makes complex data understandable

Tabular data is at the heart of scientific analysis—whether in medicine, the social sciences, or even archaeology. Making it comprehensible and usable is often a tedious task, especially when the data is extensive or complex.

techxplore.com

Felix Wiegand@fxwiegand.bsky.social · last yr.

Our paper on Datavzrd has been published in @plosone.org! 🥳 Datavzrd is a new tool written in Rust for creating interactive, shareable HTML reports from tabular data — no server needed. Check it out here: 🔗 journals.plos.org/plosone/arti... @johanneskoester.bsky.social

Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data

Tabular data, often scattered across multiple tables, is the primary output of data analyses in virtually all scientific fields. Exchange and communication of tabular data is therefore a central challenge. We present Datavzrd, a tool for creating portable, visually rich, interactive reports from tabular data in any kind of scientific discipline. Datavzrd unifies the strengths of currently common generic approaches for interactive visualization like R Shiny with the portability, ease of use and sustainability of plain spreadsheets. The generated reports do not require the maintenance of a web server nor the installation of specialized software for viewing and can simply be attached to emails, shared via cloud services, or serve as manuscript supplements. They can be specified without requiring imperative programming, thereby enabling rapid development and offering accessibility for non-computational scientists, unlocking the look and feel of dedicated manually crafted web applications without the maintenance and development burden. Datavzrd reports scale from small tables to thousands or millions of rows and offer the ability to link multiple related tables, allowing to jump between corresponding rows or hierarchically explore growing levels of detail.

journals.plos.org

Johannes Köster@johanneskoester.bsky.social · last yr.

#vembrane, our tool for filtering and transforming VCF files with easy to read Python expressions has just gained a new subcommand for directly generating #HL7 #FHIR observations from VCF records. Thanks to Till Hartmann for the continued maintenance! github.com/vembrane/vem...

GitHub - vembrane/vembrane: vembrane filters VCF records using python expressions

vembrane filters VCF records using python expressions - vembrane/vembrane

github.com

Felix Wiegand@fxwiegand.bsky.social · last yr.

🚀 We just released Alignoth v0.14.0! The HTML view now comes with a control panel, read filtering, multi-selection via shift-click, and a more interactive read info table. Check it out: github.com/alignoth/ali... #bioinformatics #rust #genomics #vegalite

GitHub - alignoth/alignoth: Creating alignment plots from bam files

Creating alignment plots from bam files. Contribute to alignoth/alignoth development by creating an account on GitHub.

github.com

Johannes Köster@johanneskoester.bsky.social · last yr.

Our preprint about #datavzrd is finally published: doi.org/10.1101/2025.... Furthermore, #datavzrd has now been downloaded 500k times. datavzrd.github.io

Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data

Tabular data, often scattered across multiple tables, is the primary output of data analyses in virtually all scientific fields. Exchange and communication of tabular data is therefore a central chall...

doi.org