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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biomformat")
In most cases, you don't need to download the package archive at all.
biomformat
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see biomformat.
An interface package for the BIOM file format
Bioconductor version: 3.3
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biomformat")
Documentation
| HTML | R Script | The biomformat package Vignette |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Metagenomics, Microbiome, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| 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 | phyloseq |
| Suggests Me | metagenomeSeq |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | biomformat_1.0.2.tar.gz |
| Windows Binary | biomformat_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | biomformat_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/biomformat/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/biomformat/ |
| Package Downloads Report | Download Stats |
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