Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

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

Material

Introduction

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

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to Transcriptomics
slides
Reference-based RNA-Seq data analysis
tutorial
De novo transcriptome reconstruction with RNA-Seq
tutorial

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
1: RNA-Seq reads to counts
tutorial
2: RNA-seq counts to genes
tutorial
3: RNA-seq genes to pathways
tutorial

Single-cell RNA-seq

Tutorials about analysis of single-cell RNA-seq data

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
An introduction to scRNA-seq data analysis
plain text
Pre-processing of Single-Cell RNA Data
plain text tutorial
Understanding Barcodes
tutorial
Plates, Batches, and Barcodes
plain text
Single-cell quality control with scater
tutorial
Downstream Single-cell RNA analysis with RaceID
tutorial
Pre-processing of 10X Single-Cell RNA Datasets
tutorial
Clustering 3K PBMCs with Scanpy
plain text tutorial
Analysis of plant scRNA-Seq Data with Scanpy
tutorial

Single-cell RNA-seq: Case Study

Tutorials using a single published single-cell RNA-seq dataset for a variety of analyses

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Generating a single cell matrix using Alevin
tutorial
Filter, Plot and Explore Single-cell RNA-seq Data
tutorial
Trajectory Analysis using Python (Jupyter Notebook) in Galaxy
tutorial

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
RNA Seq Counts to Viz in R
tutorial
Visualization of RNA-Seq results with CummeRbund
plain text tutorial
Visualization of RNA-Seq results with heatmap2
tutorial
Visualization of RNA-Seq results with Volcano Plot
tutorial
Visualization of RNA-Seq results with Volcano Plot in R
tutorial

Other


Assorted other tutorials

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
CLIP-Seq data analysis from pre-processing to motif detection
tutorial
Differential abundance testing of small RNAs
tutorial
GO Enrichment Analysis
tutorial
Network analysis with Heinz
plain text tutorial
RNA-RNA interactome data analysis
tutorial
RNA-Seq analysis with AskOmics Interactive Tool
plain text tutorial
Small Non-coding RNA Clustering using BlockClust
tutorial
Whole transcriptome analysis of Arabidopsis thaliana
plain text tutorial

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/transcriptomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

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.

Maintainers

This material is maintained by:

AvatarBérénice Batut AvatarMaria Doyle AvatarFlorian Heyl AvatarWendi Bacon

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

AvatarMaria Doyle AvatarBelinda Phipson AvatarHarriet Dashnow AvatarJovana Maksimovic AvatarAnna Trigos AvatarMatt Ritchie AvatarShian Su AvatarCharity Law AvatarFlorian Heyl AvatarDaniel Maticzka AvatarBérénice Batut AvatarMallory Freeberg AvatarIGC Bioinformatics Unit AvatarChao (Cico) Zhang AvatarFotis E. Psomopoulos AvatarToby Hodges AvatarPavankumar Videm AvatarXavier Garnier AvatarAnthony Bretaudeau AvatarAnne Siegel AvatarOlivier Dameron AvatarMateo Boudet AvatarAndrea Bagnacani AvatarCristóbal Gallardo AvatarBeatriz Serrano-Solano AvatarAnika Erxleben AvatarMarkus Wolfien AvatarMehmet Tekman AvatarWendi Bacon AvatarJonathan Manning AvatarWolfgang Maier AvatarMo Heydarian AvatarClemens Blank AvatarNicola Soranzo AvatarPeter van Heusden AvatarAlex Ostrovsky AvatarGraham Etherington AvatarHans-Rudolf Hotz AvatarDaniel Blankenberg

References