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

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

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")
colortools: devtools::install_github('gastonstat/colortools')

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:

Name		Name	Last commit message	Last commit date
Latest commit History 23 Commits
R		R
man		man
.Rbuildignore		.Rbuildignore
.gitignore		.gitignore
DESCRIPTION		DESCRIPTION
NAMESPACE		NAMESPACE
README.md		README.md
microDA.Rproj		microDA.Rproj