Applying single-cell RNA-seq analysis

Comment: What is a Learning Pathway?
A graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way
We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.

Gone is the pre-annotated, high quality tutorial data - now you have real, messy data to deal with. You have decisions to make and parameters to decide. This learning pathway challenges you to replicate a published analysis as if this were your own dataset. You will be introduced to a few more tools available for scRNA-seq in Galaxy. Finally, if our tool offerings are not enough for you, you will be directed towards how to use coding notebooks within Galaxy, setting you up to analyse scRNA-seq in R or python notebooks.

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.

For support throughout these tutorials, join our Galaxy single cell chat group on Matrix to ask questions!

New to Galaxy and/or the field of scRNA-seq? Follow this learning path to get familiar with the basics!

Module 1: Case study

These tutorials take you from raw scRNA sequencing reads to cell cluster plots to replicate a published analysis.

Lesson Slides Hands-on Recordings
Generating a single cell matrix using Alevin
Combining single cell datasets after pre-processing
Filter, plot and explore single-cell RNA-seq data with Scanpy

Module 2: Inferring trajectories

This isn’t strictly necessary, but if you want to infer trajectories - pseudotime relationships between cells - you can try out these tutorials with the same dataset. Note that you get two options for inferring trajectories, you can choose either.

Lesson Slides Hands-on Recordings
Inferring single cell trajectories with Scanpy
Inferring single cell trajectories with Monocle3

Module 3: Moving into coding environments

Did you know Galaxy can host coding environments? They don’t have the same level of computational power as the easy-to-use Galaxy tools, but you can unlock the full freedom in your data analysis. You can install your favourite single-cell tool suite that is not available on Galaxy, export your data into these coding environments and run your analysis there. If you want your favourite tool suite as a Galaxy tool, you can always request here. Let’s start with the basics of running these environments in Galaxy.

Lesson Slides Hands-on Recordings
JupyterLab in Galaxy
Use Jupyter notebooks in Galaxy
RStudio in Galaxy

The End!

And now you’re done! If you are interested in trying out the case study analyses in a coding environment, try out our “Case study: Reloaded” series next! Otherwise, you will find more features, tips and tricks in our general Galaxy Single-cell Training page.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoWendi Bacon avatar Wendi Baconorcid logoPavankumar Videm avatar Pavankumar VidemPablo Moreno avatar Pablo Moreno