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 (slides) and tutorial (tutorial) buttons below.


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



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 plain text
Understanding Barcodes tutorial
  • Plates, Batches, and Barcodes plain text

    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 tutorial
  • Combining datasets after pre-processing tutorial
    Filter, Plot and Explore Single-cell RNA-seq Data tutorial
  • Inferring Trajectories using Scanpy - Jupyter Notebook tutorial
  • Trajectory Analysis using Monocle3 plain text tutorial


    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 tutorial
  • Creating the single-cell RNA-seq reference dataset for deconvolution tutorial
    Creating the bulk RNA-seq dataset for deconvolution tutorial
    Comparing inferred cell compositions using MuSiC deconvolution tutorial

    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 plain text 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
  • 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 tutorial
    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.


    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.


    This material was contributed to by:

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