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:

Sanjay Kumar Srikakulam avatar Sanjay Kumar SrikakulamSimon Bray avatar Simon BrayMatt Ritchie avatar Matt RitchieAnton Nekrutenko avatar Anton NekrutenkoJames Taylor avatar James Taylororcid logoMira Kuntz avatar Mira KuntzOlivier Dameron avatar Olivier DameronMateusz Kuzak avatar Mateusz KuzakDaniel Maticzka avatar Daniel Maticzkaorcid logoToby Hodges avatar Toby Hodgesorcid logoMartin Čech avatar Martin ČechXi Liu avatar Xi LiuNiall Beard avatar Niall BeardMarius van den Beek avatar Marius van den BeekMarkus Wolfien avatar Markus WolfienWilliam Durand avatar William Durandorcid logoFlorian Heyl avatar Florian Heylorcid logoPeter van Heusden avatar Peter van Heusdenorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-SolanoAndrea Bagnacani avatar Andrea Bagnacaniorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal GallardoGildas Le Corguillé avatar Gildas Le Corguilléorcid logoSaskia Hiltemann avatar Saskia HiltemannJosé Manuel Domínguez avatar José Manuel Domínguezorcid logoClemens Blank avatar Clemens BlankCharity Law avatar Charity LawShian Su avatar Shian Suorcid logoWolfgang Maier avatar Wolfgang MaierMehmet Tekman avatar Mehmet Tekmanorcid logoMatti Hoch avatar Matti Hochorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoErwan Corre avatar Erwan CorreIGC Bioinformatics Unit avatar IGC Bioinformatics Unitorcid logoBjörn Grüning avatar Björn Grüningorcid logoHelena Rasche avatar Helena Rascheorcid logoClea Siguret avatar Clea Siguretorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoMateo Boudet avatar Mateo Boudetorcid logoMo Heydarian avatar Mo Heydarianorcid logoSofoklis Keisaris avatar Sofoklis KeisarisChao Zhang avatar Chao Zhangorcid logoLinelle Abueg avatar Linelle AbuegEkaterina Polkh avatar Ekaterina PolkhHarriet Dashnow avatar Harriet Dashnoworcid logoLucille Delisle avatar Lucille Delisleorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoTeresa Müller avatar Teresa Müllerorcid logoMallory Freeberg avatar Mallory Freebergorcid logoGraeme Tyson avatar Graeme Tysonorcid logoArmin Dadras avatar Armin Dadrasorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoMarek Ostaszewski avatar Marek OstaszewskiXavier Garnier avatar Xavier Garnierorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoMaria Doyle avatar Maria DoyleAnne Siegel avatar Anne Siegelorcid logoPavankumar Videm avatar Pavankumar VidemJovana Maksimovic avatar Jovana MaksimovicAnna Trigos avatar Anna TrigosBelinda Phipson avatar Belinda Phipson

Funding

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

References