metagMisc

metagMisc tools for metabarcoding and microbiome data analysis

metagMisc is an R package that provides a suite of functions for metabarcoding and microbiome data analysis (also suitable for processed metagenomic data), with particular focus on handling data in phyloseq format (McMurdie and Holmes 2013). The package helps with common workflows including data filtering, normalization, rarefaction, diversity estimation, and comparative analysis. It offers both traditional and cutting-edge approaches for handling amplicon sequencing data, making it an essential toolkit for microbial ecologists and bioinformaticians.

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")
• PhyloMeasures: remotes::install_github("cran/PhyloMeasures")
• speedyseq: remotes::install_github("mikemc/speedyseq")
• 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.

The development of this software was supported by RFBR grants 16-04-01259 and 15-29-02765.