<p>I want to grab select packages from the Bioconductor repository index. As I understand it, there are one of two ways to do this:</p>

<ol>
<li><p>Use some argument with the following repository url:  </p>

<p><code>repos = biocinstallRepos()[1]</code></p></li>
<li><p>Use some extra argument to the <code>makeDepGraph</code> function below:</p>

<p><code>z = makeDepGraph(repos)</code></p></li>
</ol>

<p>How can I specify - by name - for which packages I want to create a dependency graph?</p>

<p>Also, using Rgraphviz, how can I add the name of each package as a label?</p>

<p>TIA.</p>

<p>For your first question, take a look at the subGraph function from the graph package.  For your second, please take a look at the Rgraphviz vignette.</p>