diff --git a/.Rbuildignore b/.Rbuildignore
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--- a/.Rbuildignore
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diff --git a/docs/LICENSE.html b/docs/LICENSE.html
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@@ -23,7 +23,7 @@
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diff --git a/docs/articles/index.html b/docs/articles/index.html
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@@ -23,7 +23,7 @@
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+ <link href="../extra.css" rel="stylesheet">
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<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
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--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -9,7 +9,8 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
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+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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diff --git a/docs/authors.html b/docs/authors.html
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diff --git a/docs/extra.css b/docs/extra.css
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diff --git a/docs/index.html b/docs/index.html
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@@ -9,7 +9,8 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
+<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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@@ -82,7 +83,7 @@
<li>Functions for comparing simulations and real datasets</li>
</ul>
<p>Splatter is built on top of <a href="https://github.com/davismcc/scater"><code>scater</code></a> and stores simulations in <code>SCESet</code> objects. Splatter also has functions for comparing simulations and real datasets.</p>
-<p><strong>!Please note!</strong> This site provides documentation for the development version of Splatter. For details on the current release please refer to [<a href="https://bioconductor.org/packages/splatter" class="uri">https://bioconductor.org/packages/splatter</a>].</p>
+<p><strong>!Please note!</strong> This site provides documentation for the development version of Splatter. For details on the current release please refer to <a href="https://bioconductor.org/packages/splatter" class="uri">https://bioconductor.org/packages/splatter</a>.</p>
<div id="installation-" class="section level2">
<h2 class="hasAnchor">
<a href="#installation-" class="anchor"></a>Installation.</h2>
diff --git a/docs/news/index.html b/docs/news/index.html
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diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
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@@ -151,13 +151,13 @@ replacement) from a supplied vector.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Default generate method</span>
<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
-<span class='fu'>head</span>(<span class='fu'>fData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> Gene GeneMean Length
-#> Gene1 Gene1 1.885070e+00 2874
-#> Gene2 Gene2 5.651522e+00 1169
-#> Gene3 Gene3 1.109488e+01 2330
-#> Gene4 Gene4 8.549893e-03 4415
-#> Gene5 Gene5 5.620109e-04 7288
-#> Gene6 Gene6 4.884267e-02 4316</div><div class='input'># Sample method (human coding genes)
+<span class='fu'>head</span>(<span class='fu'>fData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> Gene GeneMean Length
+#> Gene1 Gene1 2.48516793 4364
+#> Gene2 Gene2 2.66764544 2293
+#> Gene3 Gene3 1.63746271 1981
+#> Gene4 Gene4 5.95066226 8532
+#> Gene5 Gene5 1.79688466 2083
+#> Gene6 Gene6 0.09561467 3011</div><div class='input'># Sample method (human coding genes)
</div><span class='co'># NOT RUN {</span>
<span class='fu'>library</span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
<span class='fu'>library</span>(<span class='no'>GenomicFeatures</span>)
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+ <link href="../extra.css" rel="stylesheet">
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<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 105b48431d4c03aa2684e3ad5b8562537087a223..5d8336b638dadda262bdaf5653a72a494d0b22be 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -23,7 +23,7 @@
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+ <link href="../extra.css" rel="stylesheet">
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index fbe66eda2cc6f7013ae07e870d767c9d95675556..653dd21293154347f70faadd19a531043a83336a 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -23,7 +23,7 @@
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+ <link href="../extra.css" rel="stylesheet">
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
index 065fd42b899230891f5ce8cc65f2c4c5fab07e67..3bcc5e2822d2234bdd88cae7abd1a5d43bdcb666 100644
--- a/docs/reference/splatter.html
+++ b/docs/reference/splatter.html
@@ -23,7 +23,7 @@
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+ <link href="../extra.css" rel="stylesheet">
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 8ba4119e859bfea89f58f7e63298f5c040ff04c5..c1c76331d8941568792a8d176c4a151e76c5fea1 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -23,7 +23,7 @@
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+ <link href="../extra.css" rel="stylesheet">
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -127,19 +127,19 @@ Error (RMSE) for the various properties and ranks them.</p>
<pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts..</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final SCESet...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCESets.html'>diffSCESets</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
<span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
<span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
-#> 1 Splat Mean 2.840543 NaN 1 2.850934 NaN
-#> 2 Splat Variance 11.680343 NaN 1 10.451830 NaN
-#> 3 Splat ZerosGene 40.000000 NaN 1 44.485000 NaN
-#> 4 Splat MeanVar 11.047790 NaN 1 12.143856 NaN
-#> 5 Splat MeanZeros 45.000000 NaN 1 44.780000 NaN
-#> 6 Splat LibSize 62717.000000 NaN 1 62238.650000 NaN
+#> 1 Splat Mean 2.680705 NaN 1 2.613714 NaN
+#> 2 Splat Variance 11.803596 NaN 1 10.839966 NaN
+#> 3 Splat ZerosGene 35.000000 NaN 1 41.705000 NaN
+#> 4 Splat MeanVar 11.293733 NaN 1 12.494680 NaN
+#> 5 Splat MeanZeros 45.000000 NaN 1 43.895000 NaN
+#> 6 Splat LibSize 62080.000000 NaN 1 63692.450000 NaN
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.426694 NaN 1
-#> 2 1 13.221106 NaN 1
-#> 3 1 47.795136 NaN 1
-#> 4 1 15.125288 NaN 1
-#> 5 1 54.805109 NaN 1
-#> 6 1 64042.506466 NaN 1</div></pre>
+#> 1 1 3.125188 NaN 1
+#> 2 1 13.638865 NaN 1
+#> 3 1 45.945892 NaN 1
+#> 4 1 15.583460 NaN 1
+#> 5 1 53.301735 NaN 1
+#> 6 1 64680.944707 NaN 1</div></pre>
</div>
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<h2>Contents</h2>
diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
index 55de24dc9b16647ee5c88e0ab379ed52f0a3caed..320f7ea7925795103fadf35f30a2d31adfc803e8 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -23,7 +23,7 @@
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
+ <link href="../extra.css" rel="stylesheet">
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
new file mode 100644
index 0000000000000000000000000000000000000000..5a8e0b151dcdaa45957ad85404b8e3916e56123c
--- /dev/null
+++ b/pkgdown/extra.css
@@ -0,0 +1,9 @@
+.fl {color: blue;}
+.fu {color: #00ADEF;} /* function */
+.ch,.st {color: #F47920;} /* string */
+.kw {color: #7A52C7;} /* keyword */
+.co {color: #8DC63F;} /* comment */
+
+.message { color: gray; font-weight: bolder;}
+.error { color: red; font-weight: bolder;}
+.warning { color: purple; font-weight: bolder;}