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.

Follow topic updates rss-feed with our RSS Feed

Community Resources

Community Home Maintainer Home

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 logoPeter van Heusden avatar Peter van Heusdenorcid logoMaria Doyle avatar Maria DoyleMarius van den Beek avatar Marius van den Beekorcid logoLucille Delisle avatar Lucille DelisleBelinda Phipson avatar Belinda Phipsonorcid logoMira Kuntz avatar Mira KuntzCharity Law avatar Charity Laworcid logoLinelle Abueg avatar Linelle Abuegorcid logoErwan Corre avatar Erwan Correorcid logoMartin Čech avatar Martin ČechXi Liu avatar Xi LiuMarkus Wolfien avatar Markus WolfienChao Zhang avatar Chao Zhangorcid logoHelena Rasche avatar Helena Rascheorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn GrüningJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoClemens Blank avatar Clemens BlankAnne Siegel avatar Anne Siegelorcid logoArmin Dadras avatar Armin DadrasAnna Trigos avatar Anna Trigosorcid logoMallory Freeberg avatar Mallory FreebergMatt Ritchie avatar Matt Ritchieorcid logoClea Siguret avatar Clea Siguretorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoFlorian Heyl avatar Florian HeylPeter-Bram 't Hoen avatar Peter-Bram 't HoenDaniel Maticzka avatar Daniel Maticzkaorcid logoTeresa Müller avatar Teresa Müllerorcid logoMarek Ostaszewski avatar Marek OstaszewskiXavier Garnier avatar Xavier GarnierJovana Maksimovic avatar Jovana Maksimovicorcid logoSaskia Hiltemann avatar Saskia HiltemannAndrea Bagnacani avatar Andrea BagnacaniAnton Nekrutenko avatar Anton Nekrutenkoorcid logoGraeme Tyson avatar Graeme Tysonorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMatti Hoch avatar Matti Hochorcid logoAnthony Bretaudeau avatar Anthony BretaudeauJames Taylor avatar James TaylorCharlotte Adang avatar Charlotte AdangHarriet Dashnow avatar Harriet DashnowIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoMo Heydarian avatar Mo HeydarianSimon Bray avatar Simon BraySanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamShian Su avatar Shian Suorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosEkaterina Polkh avatar Ekaterina PolkhMehmet Tekman avatar Mehmet TekmanCasper de Visser avatar Casper de Visserorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoToby Hodges avatar Toby Hodgesorcid logoMateo Boudet avatar Mateo Boudetorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoWilliam Durand avatar William Durandorcid logoNicola Soranzo avatar Nicola SoranzoMateusz Kuzak avatar Mateusz KuzakOlivier Dameron avatar Olivier DameronGildas Le Corguillé avatar Gildas Le Corguillé

Funding

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

References