#rnaseq — Public Fediverse posts

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

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

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/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

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

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

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

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/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

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

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 @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 v4.1.2 - 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

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

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

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

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

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

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

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

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

🧬 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

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."

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

"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