Single-cell Data Analysis Workshop

understanding gene signatures with amyotrophic lateral sclerosis disease (ALS)

When: Monday August 10th | 9:30am - 4:10pm

Location:
Mackenzie Room, Level 6, Charles Perkins Centre, University of Sydney
Johns Hopkins Drive, NSW 2006 Australia

Single-cell data analysis can be complex. In this data analysis workshop, we will use mouse amyotrophic lateral sclerosis (ALS) spinal cord datasets with SOD1^G93A mutation to walk through the single-cell data analysis journey including raw data preprocessing, sample quality control, batch correction and integration, automatic cell annotation, multi-sample abundance and differential expression analyses, and cell-cell interaction analysis.

We will use 10x cloud analysis, a web-based application that runs Cell Ranger to process raw sequencing data. In addition to raw sequencing data processing, we will also use the 10x cloud for both integration and batch correction. In the subsequent downstream analyses, we will use multiple tools/software, developed by 10x and the community, and get familiarized with their algorithms. After these analysis steps, we can find cell-type specific gene signatures and cell states associated with ALS disease. This workshop is tailored to users beginning their journey in single-cell data analysis.

XENIUM Data Analysis Workshop

Xenium tissue microarray data analysis with scverse

When: Tuesday August 11th | 9:30am - 4:20pm

Location:
Mackenzie Room, Level 6, Charles Perkins Centre, University of Sydney
Johns Hopkins Drive, NSW 2006 Australia

This workshop will cover in-depth analyses of Xenium data. First, we will understand Xenium technology, including Xenium decoding, Xenium Analyzer, and multi-modal cell segmentation. Then, we will learn how to evaluate Xenium data quality and use Xenium Explorer to visualize Xenium data. We will become familiar with third-party tools, primarily scverse tools, and utilize them to perform integrative analyses of Xenium data from multiple tissues, including tissue microarrays (TMA). The analyses include the loading of Xenium data and H&E image, separation of Xenium data for each sample in TMA, multi-sample integration analysis with batch correction, cell annotation, differential abundance analysis, multi-sample differential expression analysis, and conversion of each sample data to Xenium Explorer files. This workshop is tailored to users beginning their journey in Xenium data analysis.