Single Cell RNAseq: Setup

Software Installation

Installing the software may take up to 30 minutes. You may also need to contact your local Information Technology Help Desk to get permission or assistance installing the software. You may be able to install the applications using JAX Self Service software. Please do this before the workshop. We will not delay the start of the course while you install software. We will help you in advance to make sure that you have everything that you need.

If you do not already have R and RStudio installed, download and install the following software:

  1. R/4.3.1: Select the installation for your operating system (Windows, Mac, or Linux).
  2. RStudio: Download the free Rstudio Desktop.

You do not need to install this exact version of R, but it would be good to make sure your R is relatively recent (say, updated within the past year).

Once you have installed R and RStudio, open RStudio to verify that the installation was successful.

R Library Installation

In RStudio, copy and paste the following commands into the Console:

install.packages(c("tidyverse", "Matrix", "Seurat", "BiocManager", "harmony",
                   "enrichR"), dependencies = TRUE)
BiocManager::install(c("SingleCellExperiment", "scds", "DESeq2"))

Once the installation has finished, copy and paste the following commands into the console to verify that both packages installed correctly.

library(SingleCellExperiment)
library(scds)
library(tidyverse)
library(Matrix)
library(Seurat)
library(harmony)
library(enrichR)
library(DESeq2)

Project Setup

  1. Create a new project called scRNA.
    • Click the File menu button, then New Project.
    • Click New Directory.
    • Click New Project.
    • Type scRNA as the directory name. Create the project anywhere you like, but don’t forget where you put it!
    • Click the Create Project button. This will create a file called scRNA.Rproj in the directory you just created. In the future you can double-click on this file to open RStudio in this directory. This will be the easiest way to interact with the files/code you produce in this workshop.
  2. Use the Files tab to create a data folder to hold the data, a scripts folder to house your scripts, and a results folder to hold results. Alternatively, you can copy and paste the following commands into the R console for step 2 only. You still need to create a project with step 1.
dir.create("data")
dir.create("scripts")
dir.create("results")

Data Download

Before the workshop, please download the following files:

Open the scRNA.Rproj project.

download.file(url = 'https://thejacksonlaboratory.box.com/shared/static/ryxia3fm9zll20zsdzsd2nkfky4qd4ig.zip', 
              destfile = 'data/mouseStSt_exvivo.zip',
              method   = 'curl', 
              extra    = ' -L ')
download.file(url = 'https://thejacksonlaboratory.box.com/shared/static/4ijw9rxhl7bh8jev2tuoazmv8kg1iz68.zip', 
              destfile = 'data/mouseStSt_invivo.zip',
              method   = 'curl', 
              extra    = ' -L ')
download.file(url = 'https://thejacksonlaboratory.box.com/shared/static/vary3n55dso5x7lofcysgnyamw66cb0v.txt',
              destfile = 'data/regev_lab_cell_cycle_genes_mm.fixed.txt',
              method   = 'curl', 
              extra    = ' -L ')
unzip(zipfile = 'data/mouseStSt_invivo.zip' ,
      exdir   = 'data')
unzip(zipfile = 'data/mouseStSt_exvivo.zip',
      exdir   = 'data')