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 (3.14)

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 (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.21.0
In Bioconductor since BioC 3.3 (R-3.3) (5.5 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 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_1.21.0.tar.gz
Windows Binary biomformat_1.21.0.zip
macOS 10.13 (High Sierra) biomformat_1.21.0.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

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