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 (slides) and tutorial (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
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
2: RNA-seq counts to genes
3: RNA-seq genes to pathways

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
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

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
Network analysis with Heinz
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

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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Community Resources

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Editorial Board

This material is reviewed by our Editorial Board:

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

Contributors

This material was contributed to by:

orcid logoPavankumar Videm avatar Pavankumar VidemNiall Beard avatar Niall Beardorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMaria Doyle avatar Maria DoyleMateusz Kuzak avatar Mateusz KuzakJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoAnika Erxleben avatar Anika ErxlebenXi Liu avatar Xi Liuorcid logoFlorian Heyl avatar Florian HeylMehmet Tekman avatar Mehmet TekmanJovana Maksimovic avatar Jovana MaksimovicMatt Ritchie avatar Matt Ritchieorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMartin Čech avatar Martin ČechDaniel Maticzka avatar Daniel MaticzkaAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoToby Hodges avatar Toby Hodgesorcid logoAnthony Bretaudeau avatar Anthony BretaudeauOlivier Dameron avatar Olivier Dameronorcid logoLucille Delisle avatar Lucille DelisleCharity Law avatar Charity Laworcid logoClea Siguret avatar Clea SiguretAndrea Bagnacani avatar Andrea BagnacaniGildas Le Corguillé avatar Gildas Le CorguilléIGC Bioinformatics Unit avatar IGC Bioinformatics UnitMarius van den Beek avatar Marius van den Beekorcid logoHelena Rasche avatar Helena RascheBelinda Phipson avatar Belinda Phipsonorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoMallory Freeberg avatar Mallory FreebergEkaterina Polkh avatar Ekaterina Polkhorcid logoMira Kuntz avatar Mira KuntzChao Zhang avatar Chao ZhangJames Taylor avatar James Taylororcid logoMatti Hoch avatar Matti Hochorcid logoMo Heydarian avatar Mo HeydarianSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoAnne Fouilloux avatar Anne FouillouxWilliam Durand avatar William Durandorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoGraeme Tyson avatar Graeme Tysonorcid logoClemens Blank avatar Clemens Blankorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoMateo Boudet avatar Mateo BoudetHarriet Dashnow avatar Harriet Dashnoworcid logoErwan Corre avatar Erwan CorreAnna Trigos avatar Anna Trigosorcid logoWolfgang Maier avatar Wolfgang MaierMarkus Wolfien avatar Markus WolfienShian Su avatar Shian Suorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoBjörn Grüning avatar Björn GrüningXavier Garnier avatar Xavier Garnierorcid logoBérénice Batut avatar Bérénice BatutAnne Siegel avatar Anne SiegelSimon Bray avatar Simon Brayorcid logoLinelle Abueg avatar Linelle Abueg

Funding

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

References