A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
Metabarcoding is revolutionizing microbial ecology and presenting new challenges:
MetacodeR is an R package that attempts to addresses these issues:
Documentation is under construction at http://grunwaldlab.github.io/metacoder.
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:
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.
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.
plotmethod have been renamed
taxon_levelshave been replaced with
n_supertaxato make names conceptually consistent. Note that this means what was
parse_mothur_summaryfunction: parses the mothur summary table
remove_redundant_namesfunction: removes components of names of taxa in subtaxa