rpucheq / metacoder Goto Github PK

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 any file format 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 is under construction at http://grunwaldlab.github.io/metacoder_documentation.

Stable releases are available on CRAN, but the most recent version 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:

browseVignettes(package="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.

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.

This work is subject to the MIT License.