Course content
These materials were part of the ‘Single-cell RNA-seq analysis using Galaxy’ course which took place in February 2023. Please refer to the course page and programme to check details about this course and the original programme.
The content table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainers. You may proceed through the materials using the arrows at the end of each page, or pick your topic of interest from the table below to skip straight to it.
Presentation slides – View or download the slides
Recorded lectures – Watch the lecture videos
Practicals – View or download the slides, exercises, datasets, analysis scripts and results
| Format | Subject | Trainer |
| Introduction to single-cell RNA seq technologies | ||
| Keynote: The utility of Galaxy and single cell RNA-seq in personalised medicine | Andrews Stubbs |
| Experimental design of single-cell studies | Lecture | Irene Papatheodorou |
| Droplet-based library generation overview | Lecture & Activity | Wendi Bacon |
| Pipeline overview | Activity | Wendi Bacon |
| Downstream analysis | ||
| Pre-processing & batch correction | Lecture | Zhichao Miao |
| Designing your analysis | Iguaracy Pinheiro de Sousa |
| Single-cell RNA seq analysis using Galaxy | |
| Introduction to Galaxy | Lecture & Practical | Anil Thanki, Wendi Bacon, Marisa Loach, Julia Jakiela, Graeme Tyson |
| From fasta to matrix | Lecture & Practical | Iris Diana Yu, Wendi Bacon, Marisa Loach, Julia Jakiela, Graeme Tyson |
| Filter, plot & explore | Practical | Wendi Bacon |
| Trajectory analysis using Monocle 3 | Practical | Julia Jakiela, Wendi Bacon, Marisa Loach, Graeme Tyson |
| Bulk deconvolution | Practical | Mehmet Tekman, Wendi Bacon, Marisa Loach, Julia Jakiela, Graeme Tyson |
| Submitting and finding single cell data | ||
| | Singel cell data submission | Nancy George |
| | Single cell Expression Atlas | Nancy George |