Installing ALDEx, CoDaSeq, dada2, phyloseq with devtools and BiocManager - meyermicrobiolab/Meyer_Lab_Resources GitHub Wiki

Using the tools tab in RStudio, open the "Install packages" option. When the new window opens, make sure "Install dependencies" is checked (this will install additional packages required to run the specific package being installed). Type "devtools" into the "Package" blank and click "Install." devtools will allow you to install:

• Aldex2
• CoDaSeq

devtools allows packages to be pulled from the github:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ALDEx2")

library(devtools)
devtools::install_github('ggloor/CoDaSeq/CoDaSeq')

Type "BiocManager" into the "Package" blank and click "Install." BiocManager (aka Bioconductor) will allow you to install:

• dada2
• phyloseq

BiocManager::install("dada2")

BiocManager::install("ShortRead")

BiocManager::install("phyloseq")