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

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

orcid logoArmin Dadras avatar Armin Dadrasorcid logoClemens Blank avatar Clemens BlankGildas Le Corguillé avatar Gildas Le Corguilléorcid logoTeresa Müller avatar Teresa Müllerorcid logoAnika Erxleben avatar Anika ErxlebenMateusz Kuzak avatar Mateusz KuzakOlivier Dameron avatar Olivier Dameronorcid logoMatti Hoch avatar Matti Hochorcid logoCristóbal Gallardo avatar Cristóbal GallardoCasper de Visser avatar Casper de VisserMarius van den Beek avatar Marius van den Beekorcid logoPavankumar Videm avatar Pavankumar Videmorcid logoAnne Fouilloux avatar Anne FouillouxSanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamXavier Garnier avatar Xavier Garnierorcid logoMateo Boudet avatar Mateo Boudetorcid logoBjörn Grüning avatar Björn Grüningorcid logoFlorian Heyl avatar Florian HeylChao Zhang avatar Chao Zhangorcid logoPeter van Heusden avatar Peter van HeusdenMarkus Wolfien avatar Markus Wolfienorcid logoMira Kuntz avatar Mira KuntzAndrea Bagnacani avatar Andrea Bagnacaniorcid logoLinelle Abueg avatar Linelle AbuegBelinda Phipson avatar Belinda Phipsonorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh NilchiMatt Ritchie avatar Matt Ritchieorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoClea Siguret avatar Clea SiguretCharlotte Adang avatar Charlotte Adangorcid logoMaria Doyle avatar Maria Doyleorcid logoAnthony Bretaudeau avatar Anthony BretaudeauIGC Bioinformatics Unit avatar IGC Bioinformatics UnitJames Taylor avatar James TaylorAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMallory Freeberg avatar Mallory Freebergorcid logoLucille Delisle avatar Lucille Delisleorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoJosé Manuel Domínguez avatar José Manuel DomínguezDaniel Maticzka avatar Daniel MaticzkaPeter-Bram 't Hoen avatar Peter-Bram 't Hoenorcid logoHelena Rasche avatar Helena Rascheorcid logoNicola Soranzo avatar Nicola SoranzoXi Liu avatar Xi LiuSimon Bray avatar Simon BrayNiall Beard avatar Niall Beardorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoErwan Corre avatar Erwan CorreHarriet Dashnow avatar Harriet Dashnoworcid logoMartin Čech avatar Martin ČechAnna Trigos avatar Anna TrigosEkaterina Polkh avatar Ekaterina Polkhorcid logoToby Hodges avatar Toby HodgesWilliam Durand avatar William DurandCharity Law avatar Charity LawMehmet Tekman avatar Mehmet Tekmanorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoIacopo Cristoferi avatar Iacopo CristoferiJovana Maksimovic avatar Jovana Maksimovicorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMo Heydarian avatar Mo Heydarianorcid logoBérénice Batut avatar Bérénice Batutorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoWolfgang Maier avatar Wolfgang MaierAnne Siegel avatar Anne SiegelShian Su avatar Shian Su

Funding

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

References