This two half-day workshop is designed to give a general overview of the 10x and 3rd party software tools for doing multi-omics analysis of data generated using the 10x 3’ and immune profiling assays.
Day One, conducted by the 10x Support team, will provide detailed information on our Cell Ranger pipeline, covering both the theory behind each step of the analysis as well as how to execute from the command line. We will also give a demo of how our Loupe Cell Browser software can be used to visualize multiple different types of data to enable biological insight. This session will also include a short activity section at the end for each user to practice some of the skills learned during the demo.
Day Two, conducted by the Monash Bioinformatics Platform, will cover how to extend analysis to contemporary third-party tools, Seurat and Monocle. We will be walking through the 3K PBMC Dataset Tutorial and extend this to Monocle with some trajectory analysis.
Recommended Computer Requirements:
Day One: Laptop or desktop capable of running Loupe Cell Browser
Download and Installation Instructions
System Requirements
Windows
- Windows 8.1 (64-bit) or later
- 4GB RAM
- SSD storage highly recommended
- Updated video/display drivers recommended
macOS
- macOS 10.15 (Catalina) or later
- 4GB RAM
- SSD storage highly recommended
Day Two: Install latest versions of:
R
RStudio
Seurat
Monocle
Venue : Virtual workshop conducted via Zoom with breakout rooms. Zoom links will be provided after registration is complete.
Date : 13th and 14th December 2021
Day 1 Agenda (Melbourne Times):
10:00am - 10:45am: Analyzing 10x single cell gene expression and feature barcode data using Cell Ranger
10:45am - 11:30am: Additional Cell Ranger pipelines: AGGR, VDJ, Multi
11:30am - 12:00pm Experimental QC with websummary file
12:00pm - 1:00pm Lunch
1:00pm - 1:30pm Loupe Basic Overview
1:30pm - 2:00pm Advanced Loupe Functionality
2:00pm - 2:30pm Break
2:30pm - 4:00pm Loupe Cell Browser Guided Exercises (Optional)
Day 2 Agenda (Melbourne Times):
9:00am - 10:00am: Single Cell Analysis Seminar
10:00am - 11:00am: Data QC using Seurat
11:00am - 11:45am: Normalization (Seurat)
11:45am - 1:00pm: Lunch
1:00pm - 2:30pm: Dimensionality Reduction (Seurat)
2:30pm - 3:15pm: Clustering (Seurat)
3:15pm - 4:15pm: Cluster Identification (Seurat)
4:15pm - 5:30pm: Trajectory Analysis (Monocle)