Course Overview
Course Integrity
This course is compiled automatically on 2025-02-11
The course is tested and available on MacOS, Windows and
Ubuntu Linux for R 4.0
Overview
This course introduces Loupe Browser for the visualization and analysis of single cell data.
The course consists of 1 section in which we will cover all the main features of Loupe Browser including visualizing data sets, performing differntial analysis, reviewing QC and more. Each section is presented as HTML presentations or single page document. Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples.
Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/LoupeBrowser/. All material is available to download under GPL v2 license.
Setting up
System Requirements
Install Loupe Browser
Loupe Browser can be installed following the guidelines on the 10X download page
This is not essential for the training
The Presentations
Loupe Browser , Session 1
This session will show you how to:
- Check QC markers
- Review clustering
- Check marker genes
- Run differentials
- Subset the data
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Getting help
Course help
For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.
The link to the help pages can be found here
General Bioinformatics support
If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at brc@rockefeller.edu.