biomformat
This is the released version of biomformat; for the devel version, see biomformat.
An interface package for the BIOM file format
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, ImmunoOncology, Metagenomics, Microbiome, Software |
| Version | 1.40.0 |
| 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, metagenomeSeq, MGnifyR, mia, MicrobiotaProcess, MetaScope, metacoder |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | biomformat_1.40.0.tar.gz |
| Windows Binary (x86_64) | biomformat_1.40.0.zip |
| macOS Binary (big-sur-x86_64) | biomformat_1.40.0.tgz |
| macOS Binary (sonoma-arm64) | biomformat_1.40.0.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 |