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An R package for metabarcoding research planning and analysis

Metabarcoding is revolutionizing microbial ecology and presenting new challenges:

  • Numerous database formats make taxonomic data difficult to parse, combine, and subset.
  • Stacked bar charts, commonly used to depict community diversity, lack taxonomic context.
  • Barcode loci and primers are a source of under-explored bias.

MetacodeR is an R package that attempts to addresses these issues:

  • Sources of taxonomic data can be extracted from any file format and manipulated.
  • Community diversity can be visualized by color and size in a tree plot.
  • Primer specificity can be estimated with in silico PCR.

Documentation

Documentation is under construction at http://grunwaldlab.github.io/metacoder.

Download the current version

While this project is in development it can be installed through Github:

devtools::install_github(repo="grunwaldlab/metacoder", build_vignettes = TRUE)
library(metacoder)

If you've built the vignettes, you can browse them with:

browseVignettes(package="metacoder")

Dependencies

The function that runs in silico PCR requires primersearch from the EMBOSS tool kit to be installed. This is not an R package, so it is not automatically installed. Type ?primersearch after installing and loading MetcodeR for installation instructions.

Citation

We are about to submit the mansucript to a pre-print server followed by submission for peer-review. Meanwhile, cite:

ZSL Foster, TJ Sharpton and NJ Grünwald. 2016. MetacodeR: An R package for manipulation and heat tree visualization of community taxonomic data from metabarcoding. BioRxiv, to be submitted.

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Install

install.packages('metacoder')

Monthly Downloads

1,198

Version

0.1.2

License

GPL-2 | GPL-3

Maintainer

Last Published

August 26th, 2016

Functions in metacoder (0.1.2)