Transcriptomics — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

orcid logoFlorian Heyl avatar Florian Heylorcid logoBérénice Batut avatar Bérénice Batutorcid logoMaria Doyle avatar Maria Doyle

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
Sufficient Editorial Board Members Done ✅ (3 members) Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Done ✅ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Done ✅ (3 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
Learning Pathway CTA Pending ❌ By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic.

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 ✅ ✅
1: RNA-Seq reads to counts ❌ ✅ ✅ ✅
2: RNA-seq counts to genes ❌ ✅ ✅ ✅
3: RNA-seq genes to pathways ❌ ✅
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 ❌ ✅
Pathway analysis with the MINERVA Platform ✅ ✅
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 May 17, 2025 8 ✅ ❌ ❌
Reference-based RNA-Seq data analysis QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN May 17, 2025 6 ✅ ❌ ❌
Reference-based RNA-Seq data analysis QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows May 17, 2025 11 ✅ ❌ ❌
De novo transcriptome reconstruction with RNA-Seq De novo transcriptome reconstruction with RNA-Seq May 17, 2025 5 ❌ ❌ ❌
1: RNA-Seq reads to counts QC report May 17, 2025 2 ❌ ❌ ❌
1: RNA-Seq reads to counts RNA Seq Reads To Counts May 17, 2025 4 ❌ ❌ ❌
2: RNA-seq counts to genes RNA Seq Counts To Genes May 17, 2025 3 ❌ ❌ ❌
3: RNA-seq genes to pathways RNA Seq Genes To Pathways (imported from uploaded file) May 17, 2025 5 ❌ ❌ ❌
Visualization of RNA-Seq results with Volcano Plot Visualization Of RNA-Seq Results With Volcano Plot May 17, 2025 1 ✅ ✅ ❌
Visualization of RNA-Seq results with heatmap2 Heatmap2 Workflow May 17, 2025 4 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform BY-COVID: Data Download May 17, 2025 1 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform mRNA-Seq BY-COVID Pipeline: Analysis May 17, 2025 1 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform mRNA-Seq BY-COVID Pipeline: Counts May 17, 2025 1 ✅ ❌ ❌
CLIP-Seq data analysis from pre-processing to motif detection Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 May 17, 2025 8 ❌ ❌ ❌
De novo transcriptome assembly, annotation, and differential expression analysis trinity NG May 17, 2025 1 ❌ ❌ ❌
Differential abundance testing of small RNAs sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming) May 17, 2025 2 ❌ ❌ ❌
Differential abundance testing of small RNAs sRNA Seq Step 2: Salmon And DESeq2 May 17, 2025 3 ❌ ❌ ❌
GO Enrichment Analysis GO Enrichment Workflow May 17, 2025 3 ❌ ❌ ❌
Genome-wide alternative splicing analysis GTN_differential_isoform_expression May 17, 2025 3 ✅ ✅ ✅
Network analysis with Heinz Workflow Constructed From History 'Heinz Workflow Trial Sep 11' May 17, 2025 3 ❌ ❌ ❌
RNA-RNA interactome data analysis RNA-RNA interactome data analysis - chira v1.4.3 May 17, 2025 1 ✅ ❌ ❌
Small Non-coding RNA Clustering using BlockClust Blockclust 1.1.0 Clustering May 17, 2025 4 ✅ ❌ ❌
Whole transcriptome analysis of Arabidopsis thaliana Plant bulk RNA-Seq workflow May 17, 2025 3 ❌ ❌ ❌

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