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 logoBérénice Batut avatar Bérénice Batutorcid logoFlorian Heyl avatar Florian Heylorcid 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.
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Annotate Funders Done ✅ (3 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
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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 ✅ ✅
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 Apr 16, 2025 8 ✅ ❌ ❌
Reference-based RNA-Seq data analysis QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN Apr 16, 2025 6 ✅ ❌ ❌
Reference-based RNA-Seq data analysis QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows Apr 16, 2025 11 ✅ ❌ ❌
De novo transcriptome reconstruction with RNA-Seq De novo transcriptome reconstruction with RNA-Seq Apr 16, 2025 5 ❌ ❌ ❌
1: RNA-Seq reads to counts QC report Apr 16, 2025 2 ❌ ❌ ❌
1: RNA-Seq reads to counts RNA Seq Reads To Counts Apr 16, 2025 4 ❌ ❌ ❌
2: RNA-seq counts to genes RNA Seq Counts To Genes Apr 16, 2025 3 ❌ ❌ ❌
3: RNA-seq genes to pathways RNA Seq Genes To Pathways (imported from uploaded file) Apr 16, 2025 5 ❌ ❌ ❌
Visualization of RNA-Seq results with Volcano Plot Visualization Of RNA-Seq Results With Volcano Plot Apr 16, 2025 6 ✅ ❌ ❌
Visualization of RNA-Seq results with heatmap2 Heatmap2 Workflow Apr 16, 2025 4 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform BY-COVID: Data Download Apr 16, 2025 1 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform mRNA-Seq BY-COVID Pipeline: Analysis Apr 16, 2025 1 ✅ ❌ ❌
Pathway analysis with the MINERVA Platform mRNA-Seq BY-COVID Pipeline: Counts Apr 16, 2025 1 ✅ ❌ ❌
CLIP-Seq data analysis from pre-processing to motif detection Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 Apr 16, 2025 8 ❌ ❌ ❌
De novo transcriptome assembly, annotation, and differential expression analysis trinity NG Apr 16, 2025 1 ❌ ❌ ❌
Differential abundance testing of small RNAs sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming) Apr 16, 2025 2 ❌ ❌ ❌
Differential abundance testing of small RNAs sRNA Seq Step 2: Salmon And DESeq2 Apr 16, 2025 3 ❌ ❌ ❌
GO Enrichment Analysis GO Enrichment Workflow Apr 16, 2025 3 ❌ ❌ ❌
Genome-wide alternative splicing analysis GTN_differential_isoform_expression Apr 16, 2025 3 ✅ ✅ ✅
Network analysis with Heinz Workflow Constructed From History 'Heinz Workflow Trial Sep 11' Apr 16, 2025 3 ❌ ❌ ❌
RNA-RNA interactome data analysis RNA-RNA interactome data analysis - chira v1.4.3 Apr 16, 2025 1 ✅ ❌ ❌
Small Non-coding RNA Clustering using BlockClust Blockclust 1.1.0 Clustering Apr 16, 2025 4 ✅ ❌ ❌
Whole transcriptome analysis of Arabidopsis thaliana Plant bulk RNA-Seq workflow Apr 16, 2025 3 ❌ ❌ ❌

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