Installing R/RStudio

If you do not already have R/RStudio installed, do as follows.

  1. Install R
  2. Install RStudio
  3. With Windows, install also RTools (version corresponding to your R version)

Installing microbiome R package

Open R and install the package. If the installation fails, ensure from the RStudio tools panel that you have access to the Bioconductor repository.

library(BiocManager)
BiocManager::install("microbiome")

Alternatively, to install the bleeding edge (potentially unstable) development version, run in R:

library(devtools) # Load the devtools package
install_github("microbiome/microbiome") # Install the package

Using the tools

Once the package has been installed, load it in R

library(microbiome)

For a brief overview, see the package vignette and the more extensive on-line tutorial.

Further reading

General instructions to install R packages

Most R packages are maintained in CRAN, Bioconductor or Github. To install the package from each, use:

# Installing from Bioconductor
#source("http://www.bioconductor.org/biocLite.R")
BiocManager::install("MASS")

# Installing from CRAN
install.packages("sorvi")

# Installing from Github
library(devtools)
install_github("antagomir/netresponse")