biomformat

DOI: 10.18129/B9.bioc.biomformat  

An interface package for the BIOM file format

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

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

Details

biocViews	DataImport, ImmunoOncology, Metagenomics, Microbiome, Software
Version	1.26.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 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	animalcules, microbiomeExplorer, microbiomeMarker, phyloseq
Suggests Me	metagenomeSeq, mia, MicrobiotaProcess
Links To Me
Build Report

Package Archives

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

Source Package	biomformat_1.26.0.tar.gz
Windows Binary	biomformat_1.26.0.zip
macOS Binary (x86_64)	biomformat_1.26.0.tgz
macOS Binary (arm64)	biomformat_1.26.0.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