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biomformat

An interface package for the BIOM file format


Bioconductor version: Release (3.18)

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 alumni.stanford.edu> and Joseph N Paulson <jpaulson at jimmy.harvard.edu>

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

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

Installation

To install this package, start R (version "4.3") 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 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
See More
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, MetaScope, mia, MicrobiotaProcess
Links To Me
Build Report Build Report

Package Archives

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

Source Package biomformat_1.30.0.tar.gz
Windows Binary biomformat_1.30.0.zip
macOS Binary (x86_64) biomformat_1.30.0.tgz
macOS Binary (arm64) biomformat_1.30.0.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