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 most file formats 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 available at http://grunwaldlab.github.io/metacoder_documentation.

Download the current version

Stable releases are available on CRAN and can be installed in the standard way:

install.packages("metacoder")

The most recent version can be installed from Github:

devtools::install_github("grunwaldlab/metacoder@dev")
library(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

If you use metcoder in a publication, please cite our article in PLOS Computational Biology:

Foster ZSL, Sharpton TJ, Grünwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLOS Computational Biology 13(2): e1005404. https://doi.org/10.1371/journal.pcbi.1005404

License

This work is subject to the MIT License.