biomformat

DOI: 10.18129/B9.bioc.biomformat    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see biomformat.

An interface package for the BIOM file format

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("biomformat")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("biomformat")

 

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

Details

biocViews	DataImport, ImmunoOncology, Metagenomics, Microbiome, Software
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 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
Links To Me
Build Report

Package Archives

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

Source Package	biomformat_1.12.0.tar.gz
Windows Binary	biomformat_1.12.0.zip
Mac OS X 10.11 (El Capitan)	biomformat_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biomformat
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biomformat
Package Short Url	https://bioconductor.org/packages/biomformat/
Package Downloads Report	Download Stats