Single Cell Data Analysis with Partek Flow Software
Westmead Institute for Medical Research | Sydney, Australia
During this training, attendees will learn how to identify cell populations and detect differentially expressed genes in a simple single cell RNA-Seq experiment with the point-and-click interface of Partek Flow. Attendees will work with a test data set.
Afternoon tea provided
Agenda
1:00 p.m. - 4:00 p.m.
- Import a count matrix text file
- Filter cells using interactive QA/QC charts
- Filter low expressed genes
- Normalize raw count
- Visualize cell populations using the interactive 3D t-SNE plot
- Overlay gene expression and pathway signatures on the 3D t-SNE plot
- Select and classify cells on the 3D t-SNE plot
- Detect differentially expressed genes between sub-populations
- Filter a gene list
- Identify enriched KEGG pathway and/or GO terms
- Visualize cell-level results using heat maps, volcano plots, and violin plots
- Demonstrate how to import fastq files and upstream analysis pipeline on any single cell vendor prep kit
- Demonstrate how to handle CITE-Seq, feature barcoding, and cell hashing data
Bring your own internet ready laptop to participate