Pipeline release! nf-core/rnavar v1.3.0 - nf-core/rnavar 1.3.0 - Silent Nostromo!
gatk4 RNA variant calling pipeline
Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.3.0

#gatk4 #rna #rnaseq #variantcalling #worflow #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.2 - v1.1.2 - Blush Bunting!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.2

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Everytime I think that uploaded #metabolomics data can't get any weirder, I find something else.

Today, it's 1 sample out of 64 that has negative values. ONE out of 64 that has negative values. Unless something weird was done in processing, either all of them should contain negative values or none of them should. 🤦‍♂️

All missing for one sample, that sort of, might make sense. But 1 of 64 has negatives? WTF. And it's not just one value, it's 64 of 407.

#bioinformatics

I've been working on a small Julia library for working with raw nanopore sequencing signals.

It's still under development and not very mature, but maybe someone may find it useful and want to experiment with it. It provides functionality for signal-to-sequence alignments, basic signal scaling and segmentation, poly(A) tail detection, etc. If you stumble at issues or have ideas for new functionality or feedback, please reach out.

https://mzdravkov.com/docs/NanoporeSignals.jl/

#julialang #nanopore #bioinformatics

Pipeline release! nf-core/lsmquant v1.0.1 - Excited Squid Patch!
A pipeline for processing and analysis of light-sheet microscopy images.
Please see the changelog: https://github.com/nf-core/lsmquant/releases/tag/1.0.1

#3dunet #imageanalysis #imageprocessing #lightsheetmicrocopy #segmentation #stitching #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/rnafusion v4.1.3 - 4.1.3!
RNA-seq analysis pipeline for detection of gene-fusions
Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/4.1.3

#fusion #fusiongenes #genefusion #rna #rnaseq #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/magmap v1.1.0 - nf-core/magmap v1.1.0!
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Please see the changelog: https://github.com/nf-core/magmap/releases/tag/1.1.0

#nfcore #openscience #nextflow #bioinformatics

https://github.com/jwanglab/rammap A pure-Rust extensible sequence aligner and mapper mirroring the interface and producing identical output to minimap2.

#rust #minimap2 #bioinformatics

Fwd: "New paper: pyBiodatafuse: Extending interoperability of data using modular queries across biomedical resources" https://doi.org/10.59350/7n2bs-zsm80

"In a recent paper, Yojana Gadiya, Javier Millán Acosta, and Tooba Abbassi-Daloii led a project called BioDataFuse (worked on at the biohackathons of ELIXIR in 2023 and 2024 and of SWAT4HCLS in 2024 and 2025) and the matching Python package, pyBiodatafuse" https://chem-bla-ics.linkedchemistry.info/2026/05/30/new-paper-pybiodatafuse.html

Replies show up in the blog post.

#openscience #bioinformatics #python

is there a file available for download in #gtex that answers the question: "the gene/transcript G1 is most probably expressed (mRNA) in tissue T1 " ?

I'm lost in all the files available for download

edit: asked biostars: https://www.biostars.org/p/9619920/

#gtex #bioinformatics #expression #tissue #tissueBiology