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# The biomformat Package for R [![Travis-CI Build Status](]( # 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). ```S 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. ```S 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.