Training material for all kinds of transcriptomics analysis.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.


Before diving into this topic, we recommend you to have a look at:



Start here if you are new to RNA-Seq analysis in Galaxy

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
plain text
Reference-based RNA-Seq data analysis tutorial
De novo transcriptome reconstruction with RNA-Seq

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
1: RNA-Seq reads to counts tutorial
2: RNA-seq counts to genes tutorial
3: RNA-seq genes to pathways tutorial

Single-cell RNA-seq

Tutorials about analysis of single-cell RNA-seq data

Lesson Slides Hands-on Recordings Input dataset Workflows
An introduction to scRNA-seq data analysis plain text
Pre-processing of Single-Cell RNA Data plain text tutorial
Understanding Barcodes tutorial
Plates, Batches, and Barcodes plain text
Single-cell quality control with scater tutorial
Downstream Single-cell RNA analysis with RaceID tutorial
Pre-processing of 10X Single-Cell RNA Datasets tutorial
Clustering 3K PBMCs with Scanpy plain text tutorial
Analysis of plant scRNA-Seq Data with Scanpy tutorial
Bulk RNA Deconvolution with MuSiC tutorial

Single-cell RNA-seq: Case Study

Tutorials using a single published single-cell RNA-seq dataset for a variety of analyses

Lesson Slides Hands-on Recordings Input dataset Workflows
Generating a single cell matrix using Alevin tutorial
Filter, Plot and Explore Single-cell RNA-seq Data tutorial
Trajectory Analysis using Python (Jupyter Notebook) in Galaxy tutorial


Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
RNA Seq Counts to Viz in R tutorial
Visualization of RNA-Seq results with CummeRbund
plain text tutorial
Visualization of RNA-Seq results with heatmap2
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with Volcano Plot in R tutorial


Assorted other tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
CLIP-Seq data analysis from pre-processing to motif detection
Differential abundance testing of small RNAs
GO Enrichment Analysis
Network analysis with Heinz plain text tutorial
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
plain text tutorial
Small Non-coding RNA Clustering using BlockClust
Whole transcriptome analysis of Arabidopsis thaliana plain text tutorial

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.


This material is maintained by:

orcid logoAvatarBérénice Batut AvatarMaria Doyle AvatarFlorian Heyl AvatarWendi Bacon

For any question related to this topic and the content, you can contact them or visit our Gitter channel.


This material was contributed to by:

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