Single Cell

Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!). When you generate your lovely gene lists for your cells, consider checking out our Transcriptomics tutorials for further network 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 single cell analysis in Galaxy

Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
An introduction to scRNA-seq data analysis
single-cell español
Understanding Barcodes
single-cell
    • Plates, Batches, and Barcodes
    single-cell

    Case study

    These tutorials take you from raw scRNA sequencing reads to inferred trajectories to replicate a published analysis. Note you have two different options for trajectory analysis - Scanpy in Python/Jupyter Notebook, or Monocle3 in the Galaxy user interface.

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Generating a single cell matrix using Alevin
    single-cell 10x paper-replication español transcriptomics
    • Combining datasets after pre-processing
    single-cell 10x paper-replication español transcriptomics
    Filter, Plot and Explore Single-cell RNA-seq Data
    single-cell 10x paper-replication español transcriptomics
    • Inferring Trajectories using Scanpy - Jupyter Notebook
    single-cell 10x paper-replication interactive-tools transcriptomics jupyter-notebook jupyter-notebook
    • Trajectory Analysis using Monocle3
    single-cell 10x paper-replication transcriptomics

    Deconvolution

    These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Bulk RNA Deconvolution with MuSiC
    single-cell mouse human deconvolution bulk transcriptomics
    • Creating the single-cell RNA-seq reference dataset for deconvolution
    single-cell human deconvolution bulk transcriptomics
    Creating the bulk RNA-seq dataset for deconvolution
    single-cell human deconvolution bulk transcriptomics
    Comparing inferred cell compositions using MuSiC deconvolution
    single-cell mouse human deconvolution bulk transcriptomics

    End-to-end Analyses

    These tutorials use different methods to analyse scRNA-seq samples

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Pre-processing of Single-Cell RNA Data
    single-cell
    Downstream Single-cell RNA analysis with RaceID
    single-cell
    Pre-processing of 10X Single-Cell RNA Datasets
    single-cell 10x
    • Clustering 3K PBMCs with Scanpy
    single-cell 10x
    • Analysis of plant scRNA-Seq Data with Scanpy
    single-cell plants paper-replication

    • Tips, tricks & other hints

    These tutorials cover helpful skills for scRNA-seq analysis

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Single-cell quality control with scater
    single-cell
    Removing the effects of the cell cycle

    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.

    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 logoAvatarWendi BaconAvatarMehmet Tekman

    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:

    orcid logoAvatarHelena Rascheorcid logoAvatarHans-Rudolf Hotzorcid logoAvatarGraeme TysonAvatarPavankumar VidemAvatarJulia Jakielaorcid logoAvatarWolfgang Maierorcid logoAvatarDaniel Blankenbergorcid logoAvatarWendi Baconorcid logoAvatarBérénice Batutorcid logoAvatarBeatriz Serrano-Solanoorcid logoAvatarAnika Erxlebenorcid logoAvatarNicola SoranzoAvatarJonathan ManningAvatarMehmet Tekmanorcid logoAvatarCristóbal Gallardoorcid logoAvatarMarisa LoachAvatarAlex Ostrovskyorcid logoAvatarGraham EtheringtonAvatarEPSRC Training Grant DTP 2020-2021 Open University

    References