/

Installing R packages

Installing R packages

Owned by John Calder

Last updated: Oct 05, 2020

1 min read

CRAN packages you will need installed on your machine:

dirmult
BiocManager
MASS
devtools
rstan (see the instructions below for installing rstan)

To install these, run:

list.of.packages <- c("dirmult", 
                      "BiocManager", 
                      "MASS",
                      "devtools")
new.packages <-
  list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
if (length(new.packages))
  install.packages(new.packages)

Many bioinformatic packages are not on CRAN but can be installed with other tools

DADA2 is only available through BiocManager. To install it run:

BiocManager::install("dada2")

Installing rstan

If you do not have rstan already installed, please see their detailed help page here to install it. Please follow their instructions carefully

RStan Getting Started

Installing Josh's package CNVRG for testing differences in proportions

It’s now on CRAN! Woot! Woot, Josh!

install.packages("CNVRG")

Related content

Analyzing microbial count data workshop

Analyzing microbial count data workshop

Genome Technologies Laboratory

Read with this

Installing R packages on Teton

Installing R packages on Teton

Genome Technologies Laboratory

More like this

How to use Make with R and Latex

How to use Make with R and Latex

UW Data Science Center

More like this

How to install additional R packages for your use on teton

How to install additional R packages for your use on teton

UW Data Science Center

More like this

How to work in R on Teton

How to work in R on Teton

UW Data Science Center

More like this

Redo of ITS Bioinformatics for ALF1

Redo of ITS Bioinformatics for ALF1

Genome Technologies Laboratory

More like this