ACS Melbourne 2022 workshop

https://cytometryconference.org.au/

R Materials for ACS Melbourne 2022 Analytical Workflows for Single-Cell Multiomic Data workshop

Date

Sunday, Nov 20, 9am

Host

Wenyan Li

Software required

Rstudio (free version) - download and install with this link: https://posit.co/products/open-source/rstudio/

R - download and install the latest version. (Note: choose the one that matches your PC system) https://cran.csiro.au/

(encourage to try) Install R packages in Rstudio:

1. Open Rstudio
2. Inside the "Console", where you should see a welcoming message from R, showing what version of R you are using
3. type in the following line and hit enter. What this command line does is install the Seurat package if you haven't installed it already

if (!require(Seurat)) install.packages("Seurat")

4. install package tidyverse

if (!require(tidyverse)) install.packages("tidyverse")

5. install package patchwork

if (!require(patchwork)) install.packages("patchwork")

6. check if packages are installed successfully

library(Seurat)

if Seurat package doesn't exist, you will see an error message like this:

Error in library(Seurat) : there is no package called ‘Seurat’

Download demo data

1. BD Rhapsody demo data https://scomix.bd.com/hc/en-us/articles/360034192672-Rhapsody-WTA-Demo-Datasets

• download "WTA + Sample Multiplexing + AbSeq" from the list

2. 10X demo data https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-gene-expression-and-cell-surface-protein-3-standard-3-0-0

• files needed: Feature / cell matrix (filtered)