Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

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

Material

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

Introduction

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

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
Reference-based RNA-Seq data analysis
bulk rna-seq collections drosophila QC cyoa
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
collections mouse QC
2: RNA-seq counts to genes
limma-voom mouse QC
3: RNA-seq genes to pathways
mouse

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
RNA Seq Counts to Viz in R
interactive-tools
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
interactive-tools
Visualization of RNA-Seq results with heatmap2
Pathway analysis with the MINERVA Platform
bulk rna-seq viz cyoa

Other

Assorted 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
Genome-wide alternative splicing analysis
alternative splicing isoform switching
Network analysis with Heinz
metatranscriptomics network analysis
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
RNA-seq Alignment with STAR
Small Non-coding RNA Clustering using BlockClust
Whole transcriptome analysis of Arabidopsis thaliana
miRNA plants stress tolerance

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.

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Editorial Board

This material is reviewed by our Editorial Board:

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

Contributors

This material was contributed to by:

orcid logoMallory Freeberg avatar Mallory Freeberg orcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchi orcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijk orcid logoSofoklis Keisaris avatar Sofoklis Keisaris Jovana Maksimovic avatar Jovana Maksimovic orcid logoLucille Delisle avatar Lucille Delisle orcid logoCristóbal Gallardo avatar Cristóbal Gallardo orcid logoMartin Čech avatar Martin Čech orcid logoMatti Hoch avatar Matti Hoch orcid logoWolfgang Maier avatar Wolfgang Maier orcid logoFlorian Heyl avatar Florian Heyl IGC Bioinformatics Unit avatar IGC Bioinformatics Unit Harriet Dashnow avatar Harriet Dashnow orcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solano orcid logoMateo Boudet avatar Mateo Boudet Anton Nekrutenko avatar Anton Nekrutenko orcid logoMarek Ostaszewski avatar Marek Ostaszewski Belinda Phipson avatar Belinda Phipson Shian Su avatar Shian Su orcid logoErwan Corre avatar Erwan Corre orcid logoClemens Blank avatar Clemens Blank orcid logoMo Heydarian avatar Mo Heydarian Niall Beard avatar Niall Beard orcid logoBérénice Batut avatar Bérénice Batut orcid logoClea Siguret avatar Clea Siguret Gildas Le Corguillé avatar Gildas Le Corguillé James Taylor avatar James Taylor Mélanie Petera avatar Mélanie Petera José Manuel Domínguez avatar José Manuel Domínguez Xi Liu avatar Xi Liu orcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulos Daniel Maticzka avatar Daniel Maticzka orcid logoToby Hodges avatar Toby Hodges orcid logoAnne Fouilloux avatar Anne Fouilloux Ekaterina Polkh avatar Ekaterina Polkh Olivier Dameron avatar Olivier Dameron Sanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulam orcid logoPavankumar Videm avatar Pavankumar Videm Markus Wolfien avatar Markus Wolfien Mateusz Kuzak avatar Mateusz Kuzak orcid logoBjörn Grüning avatar Björn Grüning Anna Trigos avatar Anna Trigos Anne Siegel avatar Anne Siegel orcid logoPeter van Heusden avatar Peter van Heusden orcid logoMaria Doyle avatar Maria Doyle Charity Law avatar Charity Law orcid logoNate Coraor avatar Nate Coraor orcid logoIacopo Cristoferi avatar Iacopo Cristoferi orcid logoLinelle Abueg avatar Linelle Abueg orcid logoNicola Soranzo avatar Nicola Soranzo orcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotz Matt Ritchie avatar Matt Ritchie William Durand avatar William Durand Mehmet Tekman avatar Mehmet Tekman orcid logoMira Kuntz avatar Mira Kuntz Xavier Garnier avatar Xavier Garnier orcid logoAnika Erxleben avatar Anika Erxleben Marius van den Beek avatar Marius van den Beek orcid logoHelena Rasche avatar Helena Rasche Simon Bray avatar Simon Bray orcid logoGraeme Tyson avatar Graeme Tyson Teresa Müller avatar Teresa Müller orcid logoAnthony Bretaudeau avatar Anthony Bretaudeau Andrea Bagnacani avatar Andrea Bagnacani Chao Zhang avatar Chao Zhang orcid logoSaskia Hiltemann avatar Saskia Hiltemann

Funding

These individuals or organisations provided funding support for the development of this resource

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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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BeYond-COVID
BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response. This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-COVID)

References