biomformat

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 and Joseph N Paulson

Maintainer: Paul J. McMurdie

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

Installation

To install this package, start R (version "4.4") and enter:

 if (!require("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")

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

Details

biocViews	DataImport, ImmunoOncology, Metagenomics, Microbiome, Software
Version	1.32.0
In Bioconductor since	BioC 3.3 (R-3.3) (8.5 years)
License	GPL-2
Depends	R (>= 3.2), methods
Imports	plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5
System Requirements
URL	https://github.com/joey711/biomformat/ http://biom-format.org/
Bug Reports	https://github.com/joey711/biomformat/issues

Suggests	testthat (>= 0.10), knitr (>= 1.10), BiocStyle(>= 1.6), rmarkdown (>= 0.7)
Linking To
Enhances
Depends On Me
Imports Me	microbiomeExplorer, microbiomeMarker, phyloseq
Suggests Me	animalcules, metagenomeSeq, MGnifyR, mia, MicrobiotaProcess, MetaScope, metacoder
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	biomformat_1.32.0.tar.gz
Windows Binary	biomformat_1.32.0.zip
macOS Binary (x86_64)	biomformat_1.32.0.tgz
macOS Binary (arm64)	biomformat_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biomformat
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biomformat
Bioc Package Browser	https://code.bioconductor.org/browse/biomformat/
Package Short Url	https://bioconductor.org/packages/biomformat/
Package Downloads Report	Download Stats