3 R packages
“R packages are collections of functions and data sets developed by the community. They increase the power of R by improving existing base R functionalities, or by adding new ones.”1
Basically, R packages are nothing but collections of functions bundled together in a way that makes sense. Like different cookbooks that only contain recipes for a particular kind of food. They can be installed from many different sources which will be explored below.
3.1 From CRAN
The Comprehensive R Archive Network (CRAN) package repository features 18,000+ R packages. Here’s the list of Available CRAN Packages By Name. Most general purpose packages can be found here, however due to reasons, some packages are only available from other sources.
As a first example, we will download the tidyverse, a collection of R packages for data science.
“The tidyverse is an opinionated collection of R packages designed for data science. All packages share an underlying design philosophy, grammar, and data structures.”
We can install packages from CRAN with the install.packages() function like this:
install.packages("tidyverse")Note, that we can also download more than one package at once using a vector (c()) containing all package names:
install.packages(c("BiocManager", "devtools"))BiocManager as well as devtools will be used in the following to download R packages from other sources.
3.2 From Bioconductor
The Bioconductor is a collection of R packages for bioinformatics purposes. The first packages we will need from the Bioconductor will be downloaded with the install() function from the BiocManager package:
BiocManager::install(c("clusterProfiler",
"org.Hs.eg.db"
"UniProt.ws"))3.3 From GitHub and others sources
Another important source of R packages is GitHub. GitHub is not just the place where most R packages are being developed before they are put to repositories such as CRAN or Bioconductor, many other packages including the pOmics packages can be installed from it as well. :)
Let’s do it with the install_github() function from devtools:
devtools::install_github("nicohuttmann/pOmics")There are some other sources for R packages, which we want to use. Here, we are downloading the disgenet2r package to query the DisGeNET database for gene disease associations:
devtools::install_bitbucket("ibi_group/disgenet2r")