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!

What else do you want to see? You can submit tool and/or tutorial request on our Single Cell Community Tool Request Spreadsheet.

Requirements

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

• Introduction to Galaxy Analyses

Material

Introduction

Start here if you are new to single cell analysis in Galaxy and want to learn the concepts.

Your first analysis

Start here if you are new to single cell analysis in Galaxy and want to try analysing data.

Case study

These tutorials take you from raw scRNA sequencing reads to inferred trajectories to replicate a published analysis. The data is messy. The decisions are tough. The interpretation is meaningful. Come here to advance your single cell skills! Note that you get two options for inferring trajectories.

Case study: Reloaded

These tutorials let you follow the same case study analysis of real, messy data but in a programming environment, hosted on Galaxy. So if you want more flexibility, but the same guided steps as the Case Study, you can skip the Case Study and start here instead. Alternatively, try these after completing the Case Study for an easier jump to a coding environment.

End-to-end scRNA-seq Analyses

These tutorials use different methods to analyse scRNA-seq samples

Deconvolution

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

Multiomic Analyses

This section lets you build on mere scRNA analyses into a multiomic future!

Tips, tricks & other hints

These tutorials cover helpful skills for scRNA-seq analysis

Changing data formats & preparing objects

These tutorials cover a range of needs for importing data from different sources, to changing data into different formats to move from one analysis to the other.

Want to explore analysis beyond our tutorials?

Check out workflows shared by users like you!

Want to contribute?

If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single Cell Community of Practice!

• point-right Community of Practice
• feedback Matrix Chat Forum
• email Mailing List

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

Editorial Board

This material is reviewed by our Editorial Board:

Wendi Bacon

Mehmet Tekman

Pavankumar Videm

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:

Daniel Blankenberg

Marisa Loach

Wolfgang Maier

Mehmet Tekman

Cristóbal Gallardo

Morgan Howells

Alex Ostrovsky

Pavankumar Videm

Anika Erxleben

Graham Etherington

Helena Rasche

Nicola Soranzo

Graeme Tyson

Beatriz Serrano-Solano

Julia Jakiela

Camila Goclowski

Saskia Hiltemann

Hans-Rudolf Hotz

Bérénice Batut

Wendi Bacon

Jonathan Manning

Funders

This material was funded by:

ELIXIR Fair Data

EOSC-Life

EPSRC/OU

References

• Tekman, Mehmet and Batut, Bérénice; Ostrovsky, Alexander; Antoniewski, Christophe; Clements, Dave; Ramirez, Fidel; Etherington, Graham J; Hotz, Hans-Rudolf; Scholtalbers, Jelle; Manning, Jonathan R; Bellenger, Lea; Doyle, Maria A; Heydarian, Mohammad; Huang, Ni; Soranzo, Nicola; Moreno, Pablo; Mautner, Stefan; Papatheodorou, Irene; Nekrutenko, Anton; Taylor, James; Blankenberg, Daniel; Backofen, Rolf; Grüning, Björn;: A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
• Pablo Moreno, Ni Huang, Jonathan R Manning, Suhaib Mohammed, Andrey Solovyev, Krzysztof Polanski, Wendi Bacon, Ruben Chazarra, Carlos Talavera-López, Maria A Doyle, Guilhem Marnier, Björn Grüning, Helena Rasche, Nancy George, Silvie Korena Fexova, Mohamed Alibi, Zhichao Miao, Yasset Perez-Riverol, Maximilian Haeussler, Alvis Brazma, Sarah Teichmann, Kerstin B Meyer, Irene Papatheodorou;: User-friendly, scalable tools and workflows for single-cell RNA-seq analysis