Transcriptomics — Editorial Board Home

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Editorial Board

orcid logoBérénice Batut avatar Bérénice Batutorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoFlorian Heyl avatar Florian Heylorcid logoMaria Doyle avatar Maria Doyle

Action Items

Item Status Why you should do this
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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Introduction to Transcriptomics ✅ ✅
Reference-based RNA-Seq data analysis ✅ ✅ ✅
De novo transcriptome reconstruction with RNA-Seq ✅ ✅
RNA-Seq data analysis, clustering and visualisation tutorial ✅ ✅
1: RNA-Seq reads to counts ✅ ✅ ✅ ✅
2: RNA-seq counts to genes ❌ ✅ ✅ ✅
3: RNA-seq genes to pathways ❌ ✅
Pathway analysis with the MINERVA Platform ✅ ✅
RNA Seq Counts to Viz in R ✅ ✅ ✅
Visualization of RNA-Seq results with CummeRbund ❌ ✅
Visualization of RNA-Seq results with Volcano Plot ✅ ✅ ✅ ✅
Visualization of RNA-Seq results with Volcano Plot in R ❌ ✅ ✅
Visualization of RNA-Seq results with heatmap2 ✅ ✅
CLIP-Seq data analysis from pre-processing to motif detection ❌ ✅
De novo transcriptome assembly, annotation, and differential expression analysis ❌ ✅
Differential abundance testing of small RNAs ❌ ✅
GO Enrichment Analysis ❌ ✅
Genome-wide alternative splicing analysis ✅ ✅
Network analysis with Heinz ❌ ✅
RNA-RNA interactome data analysis ❌ ✅
RNA-Seq analysis with AskOmics Interactive Tool ❌ ✅ ✅
RNA-seq Alignment with STAR ✅ ✅
Reference-based RNAseq data analysis (long) ❌ ❌
Small Non-coding RNA Clustering using BlockClust ❌ ✅
Whole transcriptome analysis of Arabidopsis thaliana ❌ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Reference-based RNA-Seq data analysis DEG Part - Ref Based RNA Seq - Transcriptomics - GTN Oct 13, 2026 9 ✅ ✅ ❌
Reference-based RNA-Seq data analysis QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN Oct 13, 2026 8 ✅ ✅ ✅
Reference-based RNA-Seq data analysis QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows Oct 13, 2026 13 ✅ ✅ ❌
De novo transcriptome reconstruction with RNA-Seq De novo transcriptome reconstruction with RNA-Seq Oct 13, 2026 5 ❌ ❌ ❌
RNA-Seq data analysis, clustering and visualisation tutorial Workflow constructed from history 'Computer assignment RNA seq analysis and visualisation -BMW2 - attempt 3' Oct 13, 2026 1 ❌ ❌ ❌
1: RNA-Seq reads to counts QC report Oct 13, 2026 2 ❌ ❌ ❌
1: RNA-Seq reads to counts RNA Seq Reads To Counts Oct 13, 2026 4 ❌ ❌ ❌
2: RNA-seq counts to genes RNA Seq Counts To Genes Oct 13, 2026 3 ❌ ❌ ❌
3: RNA-seq genes to pathways RNA Seq Genes To Pathways (imported from uploaded file) Oct 13, 2026 5 ❌ ❌ ❌
Pathway analysis with the MINERVA Platform BY-COVID: Data Download Oct 13, 2026 1 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform mRNA-Seq BY-COVID Pipeline: Analysis Oct 13, 2026 1 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform mRNA-Seq BY-COVID Pipeline: Counts Oct 13, 2026 1 ✅ ❌ ❌
Visualization of RNA-Seq results with Volcano Plot Visualization Of RNA-Seq Results With Volcano Plot Oct 13, 2026 1 ✅ ✅ ❌
Visualization of RNA-Seq results with heatmap2 Heatmap2 Workflow Oct 13, 2026 5 ✅ ✅ ✅
CLIP-Seq data analysis from pre-processing to motif detection Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 Oct 13, 2026 8 ❌ ❌ ❌
De novo transcriptome assembly, annotation, and differential expression analysis trinity NG Oct 13, 2026 1 ❌ ❌ ❌
Differential abundance testing of small RNAs sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming) Oct 13, 2026 2 ❌ ❌ ❌
Differential abundance testing of small RNAs sRNA Seq Step 2: Salmon And DESeq2 Oct 13, 2026 3 ❌ ❌ ❌
GO Enrichment Analysis GO Enrichment Workflow Oct 13, 2026 3 ❌ ❌ ❌
Genome-wide alternative splicing analysis GTN_differential_isoform_expression Oct 13, 2026 3 ✅ ✅ ✅
Network analysis with Heinz Workflow Constructed From History 'Heinz Workflow Trial Sep 11' Oct 13, 2026 3 ❌ ❌ ❌
RNA-RNA interactome data analysis RNA-RNA interactome data analysis - chira v1.4.3 Oct 13, 2026 1 ✅ ❌ ❌
Small Non-coding RNA Clustering using BlockClust Blockclust 1.1.0 Clustering Oct 13, 2026 4 ✅ ❌ ❌
Whole transcriptome analysis of Arabidopsis thaliana Whole transcriptome analysis of Arabidopsis thaliana Oct 13, 2026 4 ✅ ✅ ❌

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