Installing immuneREF

Prerequisites

To be able to run the code, the following prerequisites should be fulfilled:

1. R >= 3.4.0.

2. The following packages need to be installed:

   • ggplot2
   • igraph
   • Biostrings
   • stringdist
   • vegan
   • doParallel
   • foreach
   • dplyr
   • grid
   • kebabs
   • ComplexHeatmap

# Check R version
    version[['version.string']]

# Install required R packages hosted on CRAN
    install.packages(c("ggplot2","igraph","stringdist","vegan","doParallel","foreach","dplyr","grid"))

# Install required R packages hosted on Bioconductor

    #If R version ≥ "4.0""
    if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

    BiocManager::install(c("Biostrings","kebabs","ComplexHeatmap"))

    #If R version < "4.0"
    source("https://bioconductor.org/biocLite.R")
    biocLite(c("Biostrings","kebabs","ComplexHeatmap"))

Install immuneREF

The package can be installed in R (via GitHub):

1. Check if all the prerequisites are fulfilled/installed.
2. Execute the following lines in R:

# Install the devtools package
install.packages("devtools")

# Load devtools and install immuneREF from GitHub
library(devtools)
install_github("GreiffLab/immuneREF")

# Test if installation was successful by loading immuneREF
library(immuneREF)