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 (3.21)
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("biomformat")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")
The biomformat package Vignette | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DataImport, ImmunoOncology, Metagenomics, Microbiome, Software |
Version | 1.35.0 |
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 |
See More
Suggests | testthat (>= 0.10), knitr (>= 1.10), BiocStyle(>= 1.6), rmarkdown (>= 0.7) |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | phyloseq |
Suggests Me | MGnifyR, MicrobiotaProcess, animalcules, mia, MetaScope |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | biomformat_1.35.0.tar.gz |
Windows Binary (x86_64) | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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 |