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.

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 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 Python (Jupyter Notebook) in Galaxy tutorial
Trajectory Analysis using Monocle3 plain text tutorial

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 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

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:

AvatarMehmet Tekmanorcid logoAvatarWendi Baconorcid logoAvatarBérénice Batutorcid logoAvatarAnika ErxlebenAvatarWolfgang Maierorcid logoAvatarGraham Etheringtonorcid logoAvatarNicola SoranzoAvatarAlex Ostrovskyorcid logoAvatarHans-Rudolf Hotzorcid logoAvatarDaniel Blankenbergorcid logoAvatarBeatriz Serrano-SolanoAvatarCristóbal GallardoAvatarPavankumar Videm

References