As part of the Australia and New Zealand Society for Immunology (ASI) IgV Masterclass, we will be running an online hands-on workshop (Tue 26-Oct, 10:00 am - 4:30 pm) on high-dimensional analysis approaches to investigate the immune response to COVID-19 in the blood and respiratory tract.
You are welcome to simply watch, take notes, and ask questions if you prefer! However, if you would like to follow along with the instructors to replicate the analysis process yourself using R. You will receive an email with links to the datasets and R scripts that we will use. If you did not receive the links, please email thomas.ashhurst@sydney.edu.au. Feel free to use these datasets during and after the workshop, but we would request that you don’t share these widely with others, or post them on a publicly accessible platform.
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Option 1: just join the zoom session and ask questions!
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Option 2: join the zoom session and follow along with the analysis workflow on one of our virtual computers using the provided dataset and scripts
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Option 3: join the zoom session and follow with the analysis workflow on your own computer – check out these instructions for getting setup with R/RStudio and Spectre.
Instructors
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Workshop schedule (Tue 26-Oct)
Please feel free to join us from 10:00 am to get set up with the analysis scripts and/or the virtual computers.
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Introduction Tue 26-Oct, 10:30 am - 10:45 am AEDT The workshop day (Tue 26-Oct) will start off with some opening remarks on COVID-19 and respiratory immunology from Thomas Ashhurst, Oanh Nguyen, and Katherine Kedzierska.
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Session #1: Getting started with cytometry analysis using Spectre and R Tue 26-Oct, 10:45 am – 12:00 pm AEDT Lead instructors: Givanna Putri, Felix Marsh-Wakefield In this session, instructors will introduce attendees to methods of high-dimensional analysis with R/RStudio. Specifically we will use the R package Spectre, and will explore computational approaches such as clustering (e.g. using FlowSOM) and dimensionality reduction (e.g. using tSNE or UMAP).
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Session #2: High-dimensional analysis of immune responses to COVID-19 in perhiperhal blood Tue 26-Oct, 1:00 pm – 2:30 pm AEDT Lead instructors: Felix Marsh-Wakefield, Jennifer Habel In this session we will be investigating the immune response to COVID-19 in perihperal blood. We will compare immune responses in healthy controls, convalescent patients, and patients with mild COVID-19 or severe COVID-19.
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Session #3: High-dimensional analysis of immune responses to COVID-19 in the respiratory tract Tue 26-Oct, 3:00 pm – 4:30 pm Lead instructors: Givanna Putri, Wuji Zhang In this session we will be investigating the immune response to COVID-19 in the respiratory tract, from samples acquired via an endotracheal tube. In particular we will explore a variety of myeloid cells that infiltrate the respiratory tract via the blood, including macrophages and neutrophils, and how they compare to similar cells in the blood.
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