metacoder (version 0.1.2)

metacoder: Metacoder

Description

A package for planning and analysis of amplicon metagenomics research projects.

Documentation

The full documentation can be found online at http://grunwaldlab.github.io/metacoder_documentation. There is also a short vignette included for offline use that can be accessed by the following code: browseVignettes(package = "metacoder")

Most important functions

Parseing taxonomy information:

• extract_taxonomy

Dplyr-style manipulations of taxonomic data:

• arrange_obs
• arrange_taxa
• filter_obs
• filter_taxa
• mutate_obs
• mutate_taxa
• transmute_obs
• transmute_taxa
• sample_n_obs
• sample_n_taxa
• sample_frac_obs
• sample_frac_taxa
• select_obs
• select_taxa

Taxonomically balanced sub-sampling:

• taxonomic_sample

Plotting taxonomic distribution of data:

• heat_tree

In silico PCR:

• primersearch

Details

The goal of the metacoder package is to provide a set of tools for:

• Standardized parsing of taxonomic information from diverse resources.
• A set of functions to manipulate taxonomic data modeled after dplyr.
• Visualization of statistics distributed over taxonomic classifications and phylogenies.
• Evaluating potential metabarcoding primers for taxonomic specificity.
• Evaluating potential metabarcoding loci for taxonomic discrimiation (in development).

To accomplish these goals, `metacoder` leverages resources from other R packages, interfaces with external programs, and provides novel functions where needed to allow for entire analyses within R.

To learn how to use the package and what it can do view the package vignettes by typing: browseVignettes("metacoder")