#rnaseq — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #rnaseq, aggregated by home.social.
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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/fulltext8 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).
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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/fulltext8 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).
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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!
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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!
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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!
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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!
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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!
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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/
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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/
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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
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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
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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
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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
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chatomics! tutorial: From Salmon to DESeq2: RNAseq Data Analysis https://www.youtube.com/watch?v=RWpY7EqHOUw #RNAseq
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chatomics! tutorial: From Salmon to DESeq2: RNAseq Data Analysis https://www.youtube.com/watch?v=RWpY7EqHOUw #RNAseq
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https://www.europesays.com/at/184282/ Östrogenverlust zerschneidet im Hippocampus die ECM und erhöht Alzheimer-Risiko bei Frauen #AI #Alzheimer #Aromatase #ARTIFICIALINTELLIGENCE #AT #Austria #Bioinformatik #Biomarker #Donanemab #ExtracellularMatrix #Gehirn #Geist #Gesundheit #Health #Hippocampus #Hormone #Hormontherapie #KI #KünstlicheIntelligenz #Lecanemab #Matrix #Medizin #Menopause #Neurologie #Neuroscience #Neurowissenschaften #OEstrogen #Österreich #RnaSeq #Therapie
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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 @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 @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...
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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...
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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
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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
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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
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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
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StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts
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StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts
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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 -
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 -
RE: https://mstdn.science/@nf_core/116460527673313236
kudos to my internship student who added stringtie_merge to the workflow. 🥳
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RE: https://mstdn.science/@nf_core/116460527673313236
kudos to my internship student who added stringtie_merge to the workflow. 🥳
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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