Set-up
A local installation of R (version 4.1 or greater) is required before installing RStudio. Instructions may vary based on the OS you are using (Windows, MacOS, Linux etc.). Please follow instructions found here: http://mixomics.org/wp-content/uploads/2016/09/Installation-guide-for-R-and-RStudio.pdf
Please install the following R packages through RStudio. Some dependency packages might be required for successful installation. The below packages can be installed by copying the R code into your RStudio console and running.
# Seurat
install.packages("Seurat")
library(Seurat)
# SeuratObject
install.packages("SeuratObject")
library(SeuratObject)
# Remotes
install.packages("remotes")
library(remotes)
# Install Seurat (version 5) alternative
remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE)
# tidyverse
install.packages("tidyverse")
library(tidyverse)
# msigdbr
install.packages("msigdbr")
library(msigdbr)
# SoupX
install.packages("SoupX")
library(SoupX)
# dittoSeq
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dittoSeq")
library(dittoSeq)
Downloading Workshop Data
Please follow the link to instructions on downloading data: https://rpubs.com/CKing/Downloading_Data
More information about each package can be found below.
Package |
URL |
|---|---|
Seurat* |
|
devtools* |
|
ggplot2* |
|
cellchat* |
|
dittoSeq |
https://bioconductor.org/packages/release/bioc/html/dittoSeq.html |
SoupX* |
|
msigdbr* |
https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html |
Test installation of each package using the library() function.