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README.html
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<!DOCTYPE html>
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<title>BIOM format in R</title>
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<p><link href="http://joey711.github.com/phyloseq/markdown.css" rel="stylesheet"></link></p>
<h1>BIOM format in R</h1>
<p>This is an R package for interfacing with the original JSON style <a href="http://biom-format.org/">BIOM</a> file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, 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.</p>
<p>To install the latest stable release of the biom package enter the following command from within an R session:</p>
<pre><code class="S">install.packages("biom")
</code></pre>
<p>To install the latest development version of the biom package, enter the following lines in an R session:</p>
<pre><code class="S">install.packages("devtools") # if not already installed
devtools::install_github("biom", "joey711")
</code></pre>
<ul>
<li><p>Please post feature or support requests and bugs at the <a href="https://github.com/joey711/biom/issues">issues tracker for the biom package</a> on GitHub. Issues related to the format itself and not the R interface should be posted on the <a href="https://github.com/biom-format/biom-format/issues">issues tracker for the biom format</a>.</p></li>
<li><p>Note that this is a separate (but friendly!) project from the biom-format team, and the software license is different between this package and much of the rest of the biom-format software, which has switched to BSD.</p></li>
<li><p>The offical release version of this package is <a href="http://cran.r-project.org/web/packages/biom/index.html">made available through CRAN</a>.</p></li>
</ul>
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