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 |
|---|---|---|---|---|---|
| An introduction to scRNA-seq data analysis | |||||
| Understanding Barcodes | |||||
| Plates, Batches, and Barcodes |
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.
Deconvolution
These tutorials infer cell compositions from bulk RNA-seq data using a scRNA-seq reference
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Bulk RNA Deconvolution with MuSiC | |||||
| Creating the single-cell RNA-seq reference dataset for deconvolution | |||||
| Creating the bulk RNA-seq dataset for deconvolution | |||||
| Comparing inferred cell compositions using MuSiC deconvolution |
End-to-end Analyses
These tutorials use different methods to analyse scRNA-seq samples
Tips, tricks & other hints
These tutorials cover helpful skills for scRNA-seq analysis
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Single-cell quality control with scater | |||||
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Removing the effects of the cell cycle
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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:
Wendi Bacon
Mehmet 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:
Mehmet Tekman
Alex OstrovskyWendi Bacon
EOSC-Life
Bérénice Batut
Graeme Tyson
Julia Jakiela
Helena Rasche
EPSRC Training Grant DTP 2020-2021 Open University
Anika Erxleben
Daniel Blankenberg
Beatriz Serrano-Solano
Graham Etherington
Wolfgang Maier
Pavankumar Videm
Nicola Soranzo
Hans-Rudolf Hotz
Marisa Loach
Jonathan Manning
Cristóbal Gallardo
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