To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("biomformat")

In most cases, you don't need to download the package archive at all.

biomformat

DOI: 10.18129/B9.bioc.biomformat    

This is the development version of biomformat; for the stable release version, see biomformat.

An interface package for the BIOM file format

Bioconductor version: Development (3.6)

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), 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.

Author: Paul J. McMurdie <mcmurdie at stanford.edu> and Joseph N Paulson <jpaulson at jimmy.harvard.edu>

Maintainer: Paul J. McMurdie <mcmurdie at stanford.edu>

Citation (from within R, enter citation("biomformat")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("biomformat")

Documentation

HTML R Script The biomformat package Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, Metagenomics, Microbiome, Software
Version 1.5.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License GPL-2
Depends R (>= 3.2), methods
Imports plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5
LinkingTo
Suggests testthat (>= 0.10), knitr (>= 1.10), BiocStyle(>= 1.6), rmarkdown (>= 0.7)
SystemRequirements
Enhances
URL https://github.com/joey711/biomformat/ http://biom-format.org/
BugReports https://github.com/joey711/biomformat/issues
Depends On Me
Imports Me phyloseq
Suggests Me metagenomeSeq
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package biomformat_1.5.0.tar.gz
Windows Binary biomformat_1.5.0.zip
Mac OS X 10.11 (El Capitan) biomformat_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/biomformat
Package Short Url http://bioconductor.org/packages/biomformat/
Package Downloads Report Download Stats

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