Transcriptomics

Training material for all kinds of transcriptomics analysis.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

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 Recordings Input dataset Workflows Galaxy servers
Introduction to Transcriptomics
plain text
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 Recordings Input dataset Workflows Galaxy servers
    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 Recordings Input dataset Workflows Galaxy servers
    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
  • Bulk RNA Deconvolution with MuSiC 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 Recordings Input dataset Workflows Galaxy servers
    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 Recordings Input dataset Workflows Galaxy servers
    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 Recordings Input dataset Workflows Galaxy servers
    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 AvatarAnthony Bretaudeau AvatarGildas Le Corguillé AvatarErwan Corre AvatarXi Liu AvatarMallory Freeberg AvatarIGC Bioinformatics Unit AvatarChao (Cico) Zhang AvatarAnton Nekrutenko AvatarFotis E. Psomopoulos AvatarToby Hodges AvatarErasmus+ Programme AvatarPavankumar Videm AvatarXavier Garnier 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 AvatarLucille Delisle AvatarAlex Ostrovsky AvatarGraham Etherington AvatarHans-Rudolf Hotz AvatarDaniel Blankenberg

    References