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

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