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GPLv3 License Last version CRAN_Status_Badge

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

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: