text: user982: I'm looking to generate data based on the DNA composition of a region of my genomes (data is incomplete genomes from HiSeq runs in fasta format). I'm looking for software which will give me sliding windows for GC content, GC skew, codon bias etc. I would like to use something which I can use with or plug into R. 
  
  user939: There are more R packages available that calculate GC content, for example Ape's GC.content() function.
  For example:
  > library(ape)
  > data(woodmouse)
  > GC.content(woodmouse)
  [1] 0.3873347
  
  With a sliding window is in Biostrings package.
  > library(Biostrings) 
  > DNA <- DNAString("ACTGAAACCGTGGCAGTTTGAC")
  > letterFrequencyInSlidingView(DNA, view.width=4,letters="CG")
  
  For codon usage bias, I think cubfits or sscu packages might be useful. 
  
original_text: 982: <p>I'm looking to generate data based on the DNA composition of a region of my genomes (data is incomplete genomes from HiSeq runs in fasta format). I'm looking for software which will give me sliding windows for GC content, GC skew, codon bias etc. I would like to use something which I can use with or plug into R. </p>
   939: <p>There are more R packages available that calculate GC content, for example Ape's <code>GC.content()</code> function.</p>
  
  <p>For example:</p>
  
  <pre><code>&gt; library(ape)
  &gt; data(woodmouse)
  &gt; GC.content(woodmouse)
  [1] 0.3873347
  </code></pre>
  
  <p>With a sliding window is in <code>Biostrings</code> package.</p>
  
  <pre><code>&gt; library(Biostrings) 
  &gt; DNA &lt;- DNAString("ACTGAAACCGTGGCAGTTTGAC")
  &gt; letterFrequencyInSlidingView(DNA, view.width=4,letters="CG")
  </code></pre>
  
  <p>For codon usage bias, I think <code>cubfits</code> or <code>sscu</code> packages might be useful. </p>
  