00_Installation.Rmd

---
title: "Installation"
output: html_document
---

Before you run the tutorial, you will need to install the following packages. I have written a few helper functions that will facilitate the installation process:

```{r}
# Install CRAN packages
check.packages <- function(pkg){
    new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
    if (length(new.pkg)) 
        install.packages(new.pkg, dependencies = TRUE)
    sapply(pkg, require, character.only = TRUE)
}

packages<-c("yaml", "tidyverse", "BiocManager", "umap", "ggplot2",
            "R.utils", "devtools", "")
check.packages(packages)


# Install bioconductor packages
check_biocmanager <- function(pkg){
  if (!requireNamespace(pkg, quietly = TRUE))
    install.packages(pkg)
  sapply(pkg, require, character.only = TRUE)}

packages<-c("CATALYST", "SingleCellExperiment", "flowCore", "scater", "diffcyt", "BiocParallel")
check_biocmanager(packages)

# these packages are not currently on any package manager so you will need to
# install these individually from github using devtools (installed above).

#devtools::install_github("Acribbs/siteymlgen")


```