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 () and 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
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 Galaxy servers
    1: RNA-Seq reads to counts
    2: RNA-seq counts to genes
    3: RNA-seq genes to pathways

    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
    • Pre-processing of Single-Cell RNA Data
    Understanding Barcodes
    • Plates, Batches, and Barcodes
    Single-cell quality control with scater
    Downstream Single-cell RNA analysis with RaceID
    Pre-processing of 10X Single-Cell RNA Datasets
    • Clustering 3K PBMCs with Scanpy
    • Analysis of plant scRNA-Seq Data with Scanpy
    • Bulk RNA Deconvolution with MuSiC

    • 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
    Combining datasets after pre-processing
    Filter, Plot and Explore Single-cell RNA-seq Data
    Inferring Trajectories using Python (Jupyter Notebook) in Galaxy
    Trajectory Analysis using Monocle3

    Visualisation

    Tutorials covering data visualisation

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    RNA Seq Counts to Viz in R
    • Visualization of RNA-Seq results with CummeRbund
    Visualization of RNA-Seq results with heatmap2
    Visualization of RNA-Seq results with Volcano Plot
    • Visualization of RNA-Seq results with Volcano Plot in R

    • Other


    Assorted tutorials

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

    • 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:

    orcid logoAvatarBérénice 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 orcid logoAvatarBérénice Batut orcid logoAvatarAnthony Bretaudeau AvatarGildas Le Corguillé orcid logoAvatarErwan Corre AvatarXi Liu AvatarMallory Freeberg AvatarIGC Bioinformatics Unit AvatarChao (Cico) Zhang AvatarAnton Nekrutenko orcid logoAvatarFotis E. Psomopoulos orcid logoAvatarToby Hodges AvatarErasmus+ Programme AvatarPavankumar Videm AvatarXavier Garnier AvatarAnne Siegel AvatarOlivier Dameron orcid logoAvatarMateo Boudet AvatarAndrea Bagnacani AvatarCristóbal Gallardo orcid logoAvatarBeatriz Serrano-Solano orcid logoAvatarAnika Erxleben AvatarMarkus Wolfien AvatarMehmet Tekman AvatarWolfgang Maier AvatarMo Heydarian AvatarClemens Blank orcid logoAvatarNicola Soranzo orcid logoAvatarPeter van Heusden orcid logoAvatarLucille Delisle AvatarWendi Bacon AvatarAlex Ostrovsky orcid logoAvatarGraham Etherington orcid logoAvatarHans-Rudolf Hotz orcid logoAvatarDaniel Blankenberg

    References