https://www.europesays.com/2259441/ SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics | BMC Bioinformatics ##ár #algorithms #Bioinformatics #ComputationalBiology/Bioinformatics #ComputerAppl.InLifeSciences #Data #ggplot2 #Microarrays #SCNT #SingleCellSequencing #SpatialTranscriptomics
#bioinformatics
5 posts5 participants0 posts today
ça recrute chez moi: https://umr1087.univ-nantes.fr/job-vacancies-internships/job/ingenieur-e-biologiste-en-traitement-de-donnees-bio-informaticien-ne
"Ingénieur.e biologiste en traitement de données – Bio-informaticien.ne"
UMR 1087 - L'unité de recherche de l'institut du thoraxIngénieur.e biologiste en traitement de données – Bio-informaticien.neCDD 13 mois renouvelables jusqu'à 48 mois
I have the impression that I'm the only one who wanted to load multiple data tracks in igv with one bedgraph.
I discovered it wasn't possible.
It seems easy to me to use each column of the bedgraph to make an igv track but as usual in this kind of case I must miss something.
Life Science Labs Signal Shifting Strategies Amid New Economic Pressures, According to Survey of 550+ Researchers https://www.byteseu.com/1201075/ #Bioinformatics #FinancialUncertainty #LifeScience #MarketSentiment #Science #TariffPolicies
NLM will be going through a major server maintenance from July 25th to July 28th. I'd say avoid NCBI upload/usage during that time!
https://ncbiinsights.ncbi.nlm.nih.gov/2025/07/08/ncbi-website-maintenance-july-26th/
NCBI Insights · NCBI Website Maintenance - Beginning July 25th - NCBI InsightsOn Friday, July 25th, starting at 9:00 PM EDT, we’ll be performing essential maintenance on the NLM data center. This upgrade is critical to ensure the continued reliability and stability of our services. We anticipate this planned outage will last 24 hours or more. During this time, users may experience interrupted access or degraded performance … Continue reading NCBI Website Maintenance — Beginning July 25th →
how to use #nextflow "multiMap' to transform a channel if the 'input' of an existing module doesn't fit your needs.
eg: you want
tuple val(meta), path(bam),path(bed)
while the module was designed the following way:
tuple val(meta1), path(bed)
tuple val(meta2), path(bam)
https://gist.github.com/lindenb/fbd76e5887754a7831d95422ea58f499
thanks a lot @mbp for the tip !
Gistusing nextflow multiMap to split a stream so the input can fit the design of an existing module.using nextflow multiMap to split a stream so the input can fit the design of an existing module. - multiMap.nf
Interested in learning about plant genomics? We're offering an opportunity for a few students to join our genomics team and gain hands-on experience in DNA extraction, ONT sequencing, and data analysis. Reach out if you're interested: https://www.pbb.uni-bonn.de
#Genomics #Bioinformatics #PlantScience #OpenScience
@boas_pucker
Whenever I see a DNA logo from a lab, bioinformatics/genomics centre, hackathon, or training course and it’s backwards I sigh a little. I don’t point them out anymore as I usually just receive passive aggression, but what does it say about you that you don’t care? Several big ones in my stream today. If an entomology training centre had a logo with an 8-legged fly it’d be weird right? #bioinformatics #genomics #DNA
Join the Bioconductor project at BioHackathon Europe 2025!
We're excited to be part of BioHackathon Europe 2025 (Berlin, Nov 3–7) with a project focused on improving metadata and interoperability in bioinformatics.
In-person registration closes Tuesday, July 15 - virtual participation stays open!
Project details: https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/13.md All projects: https://biohackathon-europe.org/projects/
Join the discussion in the #edam-collaboration channel on Bioconductor Zulip.
GitHubbiohackathon-projects-2025/13.md at main · elixir-europe/biohackathon-projects-2025Project descriptions for BioHackathon Europe 2025. Contribute to elixir-europe/biohackathon-projects-2025 development by creating an account on GitHub.
{targets} getting a shoutout in @kgagalova’s talk, even though the focus is on #nextflow #RStats #ReproducibleResearch #Bioinformatics #targets. #Pipelines
UCSC genome browser: "Unusually Conserved Regions - Ultracons, HARs, etc" https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&position=default&g=unusualcons
genome.ucsc.eduUnusually Conserved Track Settings
PhD students in #health, #bioinformatics, or #DataScience: this one’s for you!
Join us at Health Data Science Day 2025 on 6 November at the University of Copenhagen for a full day of:
Cutting-edge talks
Lightning talks from early-career researchers
Poster sessions
Networking across disciplines
A great chance to share your work—or get inspired for what’s next.
Deadline is 1st of October
Register now: https://lnkd.in/dPGxC4bq
Structural motif search across the protein-universe with Folddisco
https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1
I was just wondering the other day if there was already a tool to do this :) @martinsteinegger
bioRxiv · Structural motif search across the protein-universe with FolddiscoDetecting similar protein structural motifs, functionally crucial short 3D patterns, in large structure collections is computationally prohibitive. Therefore, we developed Folddisco, which overcomes this through an index of position-independent geometric features, including side-chain orientation, combined with a rarity-based scoring system. Folddisco indexes 53 million AFDB50 structures into 1.45 terabyte within 24 hours, enabling rapid detection of discontinuous or segment motifs. Folddisco is more accurate and storage-efficient than state-of-the-art methods, while being an order of magnitude faster. Folddisco is free software available at folddisco.foldseek.com and a webserver at https://search.foldseek.com/folddisco.
### Competing Interest Statement
M.S. acknowledges outside interest in Stylus Medicine. The remaining authors declare no competing interests.
National Research Foundation of Korea, https://ror.org/013aysd81, 2020M3A9G7103933, RS-2021-NR061659, RS-2021-NR056571, RS-2024-00396026, RS-2023-00250470
Novo Nordisk Foundation, https://ror.org/04txyc737, NNF24SA0092560
Just found https://genomicsclass.github.io/book/ by Rafael Irizarry and Michael Love and what a find! If you analyse genomic/transcriptomic data, that book has got you covered! #bioinformatics
genomicsclass.github.ioPH525x series - Biomedical Data Science
Pipeline release! nf-core/methylseq v4.0.0 - Wallace Chrysalis!
Please see the changelog: https://github.com/nf-core/methylseq/releases/tag/4.0.0
GitHubRelease Wallace Chrysalis · nf-core/methylseqnf-core/methylseq v4.0.0 Release Notes
This release introduces major new features, significant refactoring, and extensive test suite improvements. Key highlights include the addition of a targeted ...
#bioinformatics #microbiology #assembly question. I'm looking through some new archaeal genome assemblies, and some of the species show perfect assembly output except in one plasmid - always in about 1k different contigs of braided alternate paths but graph together nonetheless. Is this a biological signature of something?
New Bioconductor blog post!
Written during #GBCC2025 CoFest, this post highlights recent work to bring Bioconductor tools into Galaxy, featuring training materials, wrapper examples, and ideas for tool developers.
Read more 
https://blog.bioconductor.org/posts/2025-07-03-bioc-to-galaxy/
Bioconductor community blogBringing Bioconductor to Galaxy: A CoFest Collaboration – Bioconductor community blogWritten during CoFest at GBCC2025, this post shares training materials, introduces Galaxy tool wrapping, and previews what’s next for integrating Bioconductor tools in Galaxy.
Want to level up your data skills with expert support? 
Partner with #SUNDDataLab at UCPH #HeaDS for 1:1 coaching in #RStats, #Python, data wrangling & visualization.
Clean your own data. Build #ReproducibleWorkflows. Learn best practices from real Data Scientists.
Perfect for biomedical researchers ready to take charge of their data 
https://www.heads.ku.dk/datalab/
datalab@sund.ku.dk
So, redesigning a few classes in my #RStats categoryCompare2 
actually fixed all the issues I was seeing trying to manage different types of annotation enrichments, with very little effort (hypergeometric, GSEA, and binomial).
Tests are passing, just need to fix up the vignettes, and then we can merge!