metacoder (version 0.3.0)

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")

Plotting:

• heat_tree

• heat_tree_matrix

In silico PCR:

• primersearch

Analysis:

• calc_taxon_abund

• calc_obs_props

• rarefy_obs

• compare_groups

• zero_low_counts

• calc_n_samples

• filter_ambiguous_taxa

Parsers:

• parse_greengenes

• parse_mothur_tax_summary

• parse_mothur_taxonomy

• parse_newick

• parse_phyloseq

• parse_phylo

• parse_qiime_biom

• parse_rdp

• parse_silva_fasta

• parse_unite_general

Writers:

• write_greengenes

• write_mothur_taxonomy

• write_rdp

• write_silva_fasta

• write_unite_general

Database querying:

• ncbi_taxon_sample

Details

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

• Standardized parsing of taxonomic information from diverse resources.

• Visualization of statistics distributed over taxonomic classifications.

• Evaluating potential metabarcoding primers for taxonomic specificity.

• Providing flexible functions for analyzing taxonomic and abundance data.

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.