Last updated: 2021-07-07

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Introduction

In this workshop, we will introduce the data infrastructure for scRNA-seq analysis in R and practice a workflow of scRNAseq analysis; from pre-processing, quality control to dimensionality reduction and clustering, marker gene detection and cell type annotation - with plenty more along the way!

Setup requirements

We use the Bioconductor single-cell ecosystem for this workshop. Thus, participants will need a recent version of R (version 4.0+) and a set of specific packages that we use.

The code snippet below will install the necessary packages for you in R (i.e. run the following code at the R prompt in an R or RStudio session). The first line installs the BiocManager package, which is the preferred package for then installing Bioconductor packages. The next (long) line then installs the necessary Bioconductor packages (and any dependencies).

install.packages("BiocManager")
BiocManager::install(c("scRNAseq",
                       "scater",
                       "scran",
                       "clustree",
                       "BiocSingular",
                       "Rtsne",
                       "BiocFileCache",
                       "DropletUtils",
                       "EnsDb.Hsapiens.v86",
                       "schex",
                       "celldex",
                       "SingleR",
                       "gridExtra"))

If you have trouble with the package installation, please ask a colleague for help.

Once you have installed the packages, you’re ready to go with the workshop. So let’s…

Get crackin’

Follow this link for the single-cell RNA-seq analysis workflow focusing on cell type identification.


devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       macOS Big Sur 10.16         
 system   x86_64, darwin17.0          
 ui       X11                         
 language (EN)                        
 collate  en_AU.UTF-8                 
 ctype    en_AU.UTF-8                 
 tz       Australia/Melbourne         
 date     2021-07-07                  

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source        
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[1] /Users/dmccarthy/Library/R/4.0/library
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library