Metabarcoding is revolutionizing microbial ecology and presenting new challenges:
Metacoder is an R package that attempts to addresses these issues:
Documentation is available at http://grunwaldlab.github.io/metacoder_documentation.
Stable releases are available on CRAN and can be installed in the standard way:
The most recent version can be installed from Github:
devtools::install_github("grunwaldlab/[email protected]") library(metacoder)
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.
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
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