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 (3.24)
This is an R package for interfacing with the BIOM file 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 [aut, cre], Joseph N. Paulson [aut]
Maintainer: Paul J. McMurdie <joey711 at gmail.com>
citation("biomformat")):Paul J. McMurdie, Joseph N. Paulson. biomformat: An interface package for the BIOM file format. doi:10.18129/B9.bioc.biomformat, R package version 1.41.0, https://bioconductor.org/packages/biomformat.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| The biomformat package Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, ImmunoOncology, Metagenomics, Microbiome, Software |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.1), methods |
| Imports | jsonlite (>= 0.9.16), Matrix (>= 1.7-0) |
| 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), SummarizedExperiment, S4Vectors, tibble, rhdf5 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | microbiomeExplorer, phyloseq |
| Suggests Me | animalcules, iSEEtree, metacoder, metagenomeSeq, MetaScope, MGnifyR, mia, MicrobiotaProcess |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | biomformat_1.41.0.tar.gz |
| Windows Binary (x86_64) | biomformat_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | biomformat_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | biomformat_1.41.0.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 |