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The biomformat Package for R

About

This is an R package for interfacing with both the JSON and HDF5 versions of the 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.

Design

The design of this API is intended to match the python API where appropriate, while maintaining 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.

Installation

To install the latest stable release of the biomformat package enter the following in an R session (after official release).

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("biomformat")

Before official release, or to install the latest development version, enter the following into an R session.

install.packages("devtools") # if not already installed devtools::install_github("joey711/biomformat")

Support

Please post feature or support requests and bugs at the Issues Tracker for the biomformat 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 team.
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.
This package is scheduled for inclusion in the next stable release of the Bioconductor project (BioC). BioC is also where the rhdf5 package lives.
The original release of this package was made available through CRAN, as the "biom" package, supporting version 1.x (JSON) only. The current plan is to let "biom" remain on CRAN in maintenance-only mode until "biomformat" is released on Bioconductor. At which point "biom" will be considered deprecated, and eventually removed.