metagMisc

Miscellaneous functions for metagenomic analysis.

The repository is currently in ALPHA state. Nothing is guaranteed and the material is subject to change without a notice (e.g., function names or arguments).

Getting started

Vignette is under construction.

Package features

Multiple rarefaction
OTU abundance averaging following CoDa (Compositional Data Analysis) workflow
Phylogenetic diversity estimation (including standardized effect sizes)
Pairwise dissimilarity boxplots

* Prevalence plots (total OTU abundance vs OTU prevalence)

* Diversity profiles based on Hill numbers (with `entropart` package)

* Various data filtering options (e.g., extraction of the most abundant OTUs)

* Taxonomic resolution visualization

Installation

devtools::install_github("vmikk/metagMisc")

Dependencies

source("http://bioconductor.org/biocLite.R")

phyloseq: biocLite("phyloseq")
dada2: biocLite("dada2")
ALDEx2: biocLite("ALDEx2")
metagenomeSeq: biocLite("metagenomeSeq")
DESeq2: biocLite("DESeq2")
vegan: install.packages("vegan")
ggplot2
plyr
openssl

Acknowledgements

metagMisc stands on the shoulders of numerous R-packages (see Dependencies). In particular, it would not have happened without phyloseq and vegan packages. Please cite R and R packages when you use them for data analysis.