This paper presents an improved approach for mapping single-cell RNA-seq reads with optimized transcriptomic references, which markedly recovers previously missing gene expression data.
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).
The following hashtags are trending across South African Mastodon instances:
#rnaseq
#bioinformatics
#chia
#aipics
#MastodonAfrica
#church
#biblestudy
#encouragement
Based on recent posts made by non-automated accounts. Posts with more boosts, favourites, and replies are weighted higher.
The following hashtags are trending across South African Mastodon instances:
#rnaseq
#bioinformatics
#chia
#MastodonAfrica
#church
#biblestudy
#encouragement
Based on recent posts made by non-automated accounts. Posts with more boosts, favourites, and replies are weighted higher.
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!
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/
We pointed eight frontier LLMs at the same Candida auris RNA-seq study and asked each to reanalyze it on Galaxy through Orbit. Six reproduced the headline result — and the failures taught us more than the successes.
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/
We pointed eight frontier LLMs at the same Candida auris RNA-seq study and asked each to reanalyze it on Galaxy through Orbit. Six reproduced the headline result — and the failures taught us more than the successes.
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
Ming 'Tommy' Tang
nf-core
Dr. Robert M Flight
Mastodon Trends South Africa
Dave Tabb
galaxyproject
BRC Analytics