#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

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

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

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

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

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

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

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

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

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

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

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

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/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/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

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

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

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

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

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

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

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

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/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/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

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

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

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

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