BIOM format in R

This is an R package for interfacing with the original JSON style BIOM file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly “R flavor” that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

To install the latest stable release of the biom package enter the following command from within an R session:

install.packages("biom")

To install the latest development version of the biom package, enter the following lines in an R session:

install.packages("devtools") # if not already installed
devtools::install_github("biom", "joey711")

• Please post feature or support requests and bugs at the issues tracker for the biom package on GitHub. Issues related to the format itself and not the R interface should be posted on the issues tracker for the biom format.

• Note that this is a separate (but friendly!) project from the biom-format team, and the software license is different between this package and much of the rest of the biom-format software, which has switched to BSD.

• The offical release version of this package is made available through CRAN.