Chapter 3 Getting started
3.1 Checklist (before the workshop)
Install the following software in advance in order to avoid unnecessary delays and leaving more time for the workshop contents.
RStudio; choose “Rstudio Desktop” to download the latest version. Optional but preferred. For further details, check the Rstudio home page.
For Windows users: Rtools; Follow the instructions to install the toolkit. This might be required to compile some of the packages required on this course.
Install and load the required R packages
3.2 Support and resources
For online support on installation and other matters, you can join us at:
- Users: miaverse Gitter channel
- Developers: Bioconductor Slack #microbiomeexperiment channel (ask for an invitation)
3.3 Installing and loading the required R packages
This section shows how to install and load all required packages into the R session. Only uninstalled packages are installed.
if (!requireNamespace("BiocManager")) {
install.packages("BiocManager")
}
# List of packages that we need from cran and bioc
packages <- c("ggplot2", "pheatmap", "stringr", "igraph", "ANCOMBC",
"microbiome", "httpuv", "microbiomeDataSets", "mia", "caret", "ranger",
"dplyr", "miaViz", "knitr", "kableExtra", "vegan", "ecodist", "biclust",
"patchwork", "pdp", "MLmetrics", "precrec","reticulate", "MOFA2")The following script tries to load all required packages, and if they are not available, installs them.
new.pkgs <- packages[!(packages %in% installed.packages()[, "Package"])]
if (length(new.pkgs)) {
BiocManager::install(new.pkgs, ask=T)
}
sapply(packages, require, character.only = TRUE)## ggplot2 pheatmap stringr igraph
## TRUE TRUE TRUE TRUE
## ANCOMBC microbiome httpuv microbiomeDataSets
## TRUE TRUE TRUE TRUE
## mia caret ranger dplyr
## TRUE TRUE TRUE TRUE
## miaViz knitr kableExtra vegan
## TRUE TRUE TRUE TRUE
## ecodist biclust patchwork pdp
## TRUE TRUE TRUE TRUE
## MLmetrics precrec reticulate MOFA2
## TRUE TRUE TRUE TRUE