metagMisc

Miscellaneous functions for metagenomic analysis.

metagMisc package contains miscellaneous functions for metabarcoding and metagenomic analysis, including data transformations, several parsers (for USERCH UC-format; BLAST, SINA and STAMPA outputs, etc.), taxonomy handlers (SILVA, QIIME, AMPTk), phyloseq-shortcuts (multiple rarefaction, phyloseq splitting and exporting), and DADA2-shortcuts (error rate estimation on the subset of data, export of denoised amplicons in fasta).

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.

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