microDA

R package with expanded applications of classic R functions for microbiome datasets

This repository contains miscellaneous functions for microbiome data analysis using utilities from other packages. Still in ALPHA state.

Getting started

Installation

install.packages("devtools")
devtools::install_github("alopgar/microDA")

Dependencies

• tidyverse: install.packages("tidyverse")
• microbiome: BiocManager::install("microbiome") or devtools::install_github("microbiome/microbiome")
• phyloseq: source('http://bioconductor.org/biocLite.R'); biocLite('phyloseq')
• vegan: install.packages("vegan")
• nortest: install.packages("nortest")
• DESeq2: BiocManager::install("DESeq2")
• ALDEx2: BiocManager::install("ALDEx2")
• sunburstR: install.packages("sunburstR")
• ellipse: install.packages("ellipse")
• VennDiagram: install.packages("VennDiagram")
• ggrepel: install.packages("ggrepel")
• ggordiplots: remotes::install_github("jfq3/ggordiplots")

Acknowledgements

This repository uses functions from multiple R packages. Please cite R and those R packages when using it.

Some included functions have been adapted from other public repositories:

• get_max_taxonomic_rank: From metagMisc
• phyloseq_to_df: From metagMisc
• CIplot_biv: From easyCODA