#rnaseq — Public Fediverse posts

Today we just added 4195 human gene expression studies to the dee2.io data resource -- that is ~200k samples. We're still running way behind what is released by NCBI, but with the current prices of computer parts we're doing the best we can with the limited funding we got.
#rnaseq #bioinformatics #genomics

Bioinformatician - Lung Cancer Omics and Biomarkers
IRCCS Casa della Sofferenza Foundation

See the full job description on jobRxiv: https://jobrxiv.org/job/irccs-casa-della-sofferenza-foundation-27778-bioinformatician-lung-cancer-omics-and-biomarkers/

#bioinformatics #biomarkers #lungcancer #RNAseq #spatialbiology #ScienceJobs #hiring #research
https://jobrxiv.org/job/irccs-casa-della-sofferenza-foundation-27778-bioinformatician-lung-cancer-omics-and-biomarkers/?fsp_sid=14608

Pipeline release! nf-core/scrnaseq v4.2.0 - 4.2.0!
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.2.0

#10xgenomics #10xgenomics #alevin #bustools #cellranger #kallisto #rnaseq #singlecell #starsolo #nfcore #openscience #nextflow #bioinformatics

6/ Lastly, in https://www.nature.com/articles/s41592-023-02003-w. the observed sensitivity deficits stem from three sources: (1) poor annotation of 3′ gene ends; (2) issues with intronic read incorporation; and (3) gene overlap-derived read loss. #singlecell #RNAseq

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/differentialabundance v2.0.0 - v2.0.0 - 2026-06-23!
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Please see the changelog: https://github.com/nf-core/differentialabundance/releases/tag/2.0.0

#atacseq #chipseq #deseq2 #differentialabundance #differentialexpression #gsea #limma #microarray #rnaseq #shiny #nfcore #openscience #nextflow #bioinformatics

New co-authored manuscript on liver cancer multi-omics:

Integrated Multi-omic Analyses Reveal Novel Gene-Metabolite Relationships in Human Steatohepatitic Hepatocellular Carcinoma
Anspach et al., https://www.jlr.org/article/S0022-2275(26)00107-0/fulltext

8 patients, *paired samples* of cancer and adjacent normal!! (made the statistics so nice to work with and look for correlations between rna-seq and metabolomics).

#Bioinformatics #Metabolomics #RNASeq

When I first tried to assemble transcripts from #RNASeq data, I often wished for a handy overview of the #bioinformatics pipeline, from acquiring sequencer data to attaching descriptions to protein sequences. This video is my attempt to fill that gap, building upon our 2021 paper identifying proteins in #chia (Salvia hispanica) based on assembled transcript sequences. I hope you enjoy it!

https://www.youtube.com/watch?v=ZtJWaWrTXyA

Eight frontier LLMs, one RNA-seq dataset. We had them reproduce a published Candida auris analysis by using Orbit to drive Galaxy.

Six models independently replicated the original SCF1 downregulation finding—while their API costs varied 47× ($2.82–$131.83).

Read what we learned: https://galaxyproject.org/news/2026-06-09-llm-agents-reanalyze-rnaseq/

#UseGalaxy #RNAseq #AI #LLM #Bioinformatics

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/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

chatomics! tutorial: From Salmon to DESeq2: RNAseq Data Analysis https://www.youtube.com/watch?v=RWpY7EqHOUw #RNAseq

Kind of nuts that one can make all of these cards for offloading with clang (AMD requires cosplaying as a different architecture) via @openmp_arb

True performance portability
#GPU #openmp
Time to try slorado now #RNAseq!
https://www.amd.com/en/blogs/2025/breaking-barriers-in-genomics.html
https://www.biorxiv.org/content/10.64898/2026.03.25.714356v1

Kind of nuts that one can make all of these cards for offloading with clang (AMD requires cosplaying as a different architecture) via @[email protected] . True performance portability #GPU #openmp Time to try slorado now #RNAseq! www.amd.com/en/blogs/202... www.biorxiv.org/content/10.6...

Pipeline release! nf-core/rnafusion v4.1.2 - 4.1.2!
RNA-seq analysis pipeline for detection of gene-fusions
Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/4.1.2

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

Pipeline release! nf-core/rnafusion v4.1.1 - 4.1.1!
RNA-seq analysis pipeline for detection of gene-fusions
Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/4.1.1

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

StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts

https://www.nature.com/articles/s41592-026-03080-3.epdf

#rnaseq #totalrnaseq #bioinformatics

Low-hanging fruit: everyone sees it, few actually pick it up 🍎🍇🍉🍓🫐🍒

Our latest preprint explores dark pigmentation in blackberry, a plant characterized by low-hanging fruit. The combination of genomics and transcriptomics reveals insights into the genetics of pigment biosynthesis. High levels of cyanidin-3-O-glucoside were identified in blackberries, which may explain their dark coloration.

Read more: https://doi.org/10.64898/2026.05.05.723051

#PlantSciences #Pigments #Fruits #Genomics #RNAseq
@PuckerLab

Pipeline release! nf-core/rnaseq v3.26.0 - nf-core/rnaseq v3.26.0 - Chromium Cuttlefish!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.26.0

#rna #rnaseq #nfcore #openscience #nextflow #bioinformatics

RE: https://mstdn.science/@nf_core/116460527673313236

kudos to my internship student who added stringtie_merge to the workflow. 🥳

#nfcore #rnaseq #nextflow

Pipeline release! nf-core/rnaseq v3.25.0 - nf-core/rnaseq v3.25.0 - Plutonium Pangolin!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.25.0

#rna #rnaseq #nfcore #openscience #nextflow #bioinformatics

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)

🔗Registration form link: https://lnkd.in/gQcHggGF

#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats

Pipeline release! nf-core/rnaseq v3.24.0 - nf-core/rnaseq v3.24.0 - Selenium Seahorse!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.24.0

#rna #rnaseq #nfcore #openscience #nextflow #bioinformatics

🧬 Can AI truly decode gene expression, or is it being misled by too much data?

🔗 Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0039

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#ArtificialIntelligence #MachineLearning #Bioinformatics #Genomics #RNAseq #ComputationalBiology #SystemsBiology #AI #PrecisionMedicine #BigData #AIinHealthcare

If you are someone who has ever thought running a bunch of samples through recount3 on your own hardware is a good idea, and you are horrid at writing shell scripts to manage it all, I've created a little #RStats package that helps with:

- running samples through recount-pump and unify;
- copying unify outputs into a directory that recount3 will see and load;
- checking your fq.gz files to make sure they aren't bad before running pump.

https://moseleybioinformaticslab.github.io/rc3helpers/

#Bioinformatics #RNASeq

dupRadar keeps breaking @nf_core #rnaseq runs. So as a bit of a joke, I prompted #Claude Code + Seqera AI to rewrite it in Rust. My Slack message:

"I did a rust rewrite over lunch. I realize that I might have accidentally also made a super fast Rust implementation of featureCounts."

"Cellular morphology emerges from polygenic, distributed transcriptional variation", Paylakhi et al. 2026
https://www.biorxiv.org/content/10.64898/2026.03.12.711281v1

#CellBiology #transcriptomics #CellPainting #RNAseq

Pipeline release! nf-core/rnafusion v4.1.0 - 4.1.0!

Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/4.1.0

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

STAR Suite: Integrating transcriptomics through AI software engineering in the NIH MorPhiC consortium https://www.biorxiv.org/content/10.64898/2026.03.09.710580v1

" In just four months, a single developer added over 92,000 lines to the original 28,000-line codebase to produce four unified modules: STAR-core, STAR-Flex, STAR-Perturb, and STAR-SLAM that can be installed as a pre-compiled binary without introducing any new dependencies. "

#AI #rnaseq