Installation

It is advised not to have any packages loaded when installing DAtest.

First install DAtest:

if (!requireNamespace("devtools")) install.packages("devtools")

# Developmental version (recommended):
devtools::install_github("Russel88/DAtest")

# Version associated with bioRxiv paper:
# devtools::install_github("Russel88/[email protected]")

Main difference between bioRxiv version and developmental version is that the developmental version includes a "Score" that can be used to rank the different methods. This Score is a combination of False Discovery Rate (FDR), spike detect rate (empirical power) and Area under the ROC Curve (AUC). The general approach is still the same as described in the paper. The developmental version also includes additional methods and several bug fixes. See details on the changes here.

The following packages are suggested and are needed for full functionality

if (!requireNamespace("BiocManager")) install.packages("BiocManager")

BiocManager::install(c("DESeq2","limma","edgeR","metagenomeSeq","baySeq","ALDEx2","impute","ANCOMBC"))

install.packages(c("samr","pscl","statmod","mvabund"))

Note: If installation fails for any of these additional packages, do not despair. DAtest will work seamlessly, but will simply exclude methods that depends on these packages.

The following are suggested, but not needed:

# For drawing Venn diagrams
install.packages("eulerr")

# For post-hoc testing (generalized) linear models
install.packages("lsmeans")

# Phyloseq, for organizing microbiome data
BiocManager::install("phyloseq")