From 1cb24343c3bcadd64184ab3ff84623b4075589b8 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 4 Aug 2017 16:08:14 +1000
Subject: [PATCH] Add index.md
---
docs/index.html | 52 +++++++++-----------
docs/reference/addGeneLengths.html | 14 +++---
docs/reference/lunEstimate.html | 2 +-
docs/reference/setParam.html | 2 +-
docs/reference/setParams.html | 6 +--
docs/reference/simpleEstimate.html | 2 +-
docs/reference/splatEstimate.html | 2 +-
docs/reference/summariseDiff.html | 26 +++++-----
index.md | 79 ++++++++++++++++++++++++++++++
9 files changed, 129 insertions(+), 56 deletions(-)
create mode 100644 index.md
diff --git a/docs/index.html b/docs/index.html
index 1ee41a9..7a16a9b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -71,9 +71,7 @@
</header><div class="row">
<div class="contents col-md-9">
- <div id="splatter" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#splatter" class="anchor"></a>Splatter</h1></div>
+
<p><img src="https://s16.postimg.org/xc6u52b0l/splatter_logo_small.png" alt="Splatter logo"></p>
<p>Splatter is an R package for the simple simulation of single-cell RNA sequencing data. Splatter provides a common interface to multiple simulations that have:</p>
@@ -81,46 +79,39 @@
<li>Functions for estimating simulation parameters</li>
<li>Objects for storing those parameters</li>
<li>Functions for simulating counts using those parameters</li>
+<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>
<div id="installation-" class="section level2">
<h2 class="hasAnchor">
<a href="#installation-" class="anchor"></a>Installation.</h2>
-<div id="development-version" class="section level3">
+<div id="release-version" class="section level3">
<h3 class="hasAnchor">
-<a href="#development-version" class="anchor"></a>Development version</h3>
-<p>Splatter has been accepted into the latest version of <a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html">Bioconductor</a> and hence requires the latest version of R (>=3.4).</p>
+<a href="#release-version" class="anchor"></a>Release version</h3>
+<p>Splatter has been accepted into the latest version of <a href="https://bioconductor.org/packages/splatter">Bioconductor</a> and hence requires the latest version of R (>=3.4).</p>
<p>If you have these installed Splatter can be installed from Bioconductor using <code>biocLite</code>:</p>
<pre class="{r}"><code>source("https://bioconductor.org/biocLite.R")
biocLite("splatter")</code></pre>
<p>If you wish to build a local version of the vignette use:</p>
-<pre class="{r}"><code>biocLite("splatter", build_vignettes=TRUE)</code></pre>
+<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/BiocInstaller/topics/biocLite">biocLite("splatter", build_vignettes=TRUE)</a></code></pre>
<p>This will also build the vignette and install all suggested dependencies (which aren’t required for core functionality). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.</p>
</div>
-</div>
-<div id="getting-started" class="section level2">
-<h2 class="hasAnchor">
-<a href="#getting-started" class="anchor"></a>Getting started</h2>
-<p>Once installed the best place to get started is the vignette. For most users the most convient way to access this is online <a href="https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html">here</a>.</p>
-<p>Alternatively, if you chose to build the vignette, you can load Splatter, then browse the vignettes:</p>
-<pre class="{r}"><code>library(splatter)
-browseVignettes("splatter")</code></pre>
-<p>This is a detailed document that introduces the main features of Splatter.</p>
-</div>
-<div id="citing-splatter" class="section level2">
-<h2 class="hasAnchor">
-<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h2>
-<p>If you use Splatter please cite our paper <a href="http://dx.doi.org/10.1101/133173">“Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA Sequencing Data. bioRxiv. 2017; doi:10.1101/133173â€</a>.</p>
-<pre><code>@Article{,
- author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
- title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
- journal = {bioRxiv},
- year = {2017},
- url = {http://dx.doi.org/10.1101/133173},
- doi = {10.1101/133173},
- }</code></pre>
+<div id="development-version" class="section level3">
+<h3 class="hasAnchor">
+<a href="#development-version" class="anchor"></a>Development version</h3>
+<p>If you want to try the [development version][deve] this can also be installed from Bioconductor:</p>
+<pre class="{r}"><code>library(BiocInstaller)
+useDevel()
+biocValid() # checks for out of date packages
+biocLite() # (optional) updates out of date packages
+biocLite("splatter")</code></pre>
+<p>Depending on the current release cycle you may also need to install the development version of R. See <a href="https://www.bioconductor.org/developers/how-to/useDevel/">here</a> for more details.</p>
+<p>Alternatively the development version can be installed directly from <a href="https://github.com/Oshlack/splatter">Github</a>:</p>
+<pre class="{r}"><code><a href="http://www.rdocumentation.org/packages/devtools/topics/install">devtools::install("Oshlack/splatter")</a></code></pre>
</div>
</div>
+
</div>
<div class="col-md-3" id="sidebar">
@@ -150,6 +141,9 @@ browseVignettes("splatter")</code></pre>
<li><a href="https://travis-ci.org/Oshlack/splatter"><img src="https://travis-ci.org/Oshlack/splatter.svg?branch=master" alt="Travis-CI Build Status"></a></li>
<li><a href="https://codecov.io/github/Oshlack/splatter?branch=master"><img src="https://img.shields.io/codecov/c/github/Oshlack/splatter/master.svg" alt="Coverage Status"></a></li>
<li><a href="https://ci.appveyor.com/project/Oshlack/splatter"><img src="https://ci.appveyor.com/api/projects/status/github/Oshlack/splatter?branch=master&svg=true" alt="AppVeyor Build Status"></a></li>
+<li><a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html"><img src="https://bioconductor.org/shields/years-in-bioc/splatter.svg" alt="Bioconductor History"></a></li>
+<li><a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html"><img src="https://bioconductor.org/shields/build/devel/bioc/splatter.svg" alt="Bioconductor Status"></a></li>
+<li><a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html"><img src="https://bioconductor.org/shields/downloads/splatter.svg" alt="Bioconductor Downloads"></a></li>
</ul>
</div>
</div>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index f0ff3b8..e4e7505 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -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 0.11722336 1472
-#> Gene2 Gene2 0.06408871 1265
-#> Gene3 Gene3 0.94493523 5846
-#> Gene4 Gene4 0.01420334 869
-#> Gene5 Gene5 0.88761646 10791
-#> Gene6 Gene6 0.51893805 7501</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 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)
</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>)
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 751c6cf..888bcdb 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -146,7 +146,7 @@ for more details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 759115
+#> 2000 40 269882
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index e480024..9a5c2bc 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -151,7 +151,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 759115
+#> 100 100 269882
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index f92af13..d8e2583 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -146,7 +146,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (Genes) (Cells) [Seed]
-#> 10000 100 759115
+#> 10000 100 269882
#>
#> 3 additional parameters
#>
@@ -164,7 +164,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 759115
+#> 1000 50 269882
#>
#> 3 additional parameters
#>
@@ -182,7 +182,7 @@ them manually), see examples.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 1000 50 759115
+#> 1000 50 269882
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index aaef5dd..4455a8b 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -148,7 +148,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 759115
+#> 2000 40 269882
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 1b4973b..5111395 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -148,7 +148,7 @@ data to estimate parameters from.</p></td>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 759115
+#> 2000 40 269882
#>
#> 27 additional parameters
#>
diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 20d29a9..8ba4119 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -126,20 +126,20 @@ Error (RMSE) for the various properties and ranks them.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<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 2.08877 NaN 1 2.280154 NaN
-#> 2 Splat Variance 11.60810 NaN 1 10.409312 NaN
-#> 3 Splat ZerosGene 30.00000 NaN 1 37.835000 NaN
-#> 4 Splat MeanVar 11.27607 NaN 1 12.092148 NaN
-#> 5 Splat MeanZeros 40.00000 NaN 1 40.810000 NaN
-#> 6 Splat LibSize 58036.50000 NaN 1 57569.750000 NaN
+<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
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 2.779126 NaN 1
-#> 2 1 12.936623 NaN 1
-#> 3 1 42.628336 NaN 1
-#> 4 1 15.034437 NaN 1
-#> 5 1 50.112374 NaN 1
-#> 6 1 58351.247110 NaN 1</div></pre>
+#> 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>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/index.md b/index.md
new file mode 100644
index 0000000..1af5f09
--- /dev/null
+++ b/index.md
@@ -0,0 +1,79 @@
+[](https://travis-ci.org/Oshlack/splatter)
+[](https://codecov.io/github/Oshlack/splatter?branch=master)
+[](https://ci.appveyor.com/project/Oshlack/splatter)
+[](https://bioconductor.org/packages/devel/bioc/html/splatter.html)
+[](https://bioconductor.org/packages/devel/bioc/html/splatter.html)
+[](https://bioconductor.org/packages/devel/bioc/html/splatter.html)
+
+
+
+Splatter is an R package for the simple simulation of single-cell RNA sequencing
+data. Splatter provides a common interface to multiple simulations that have:
+
+* Functions for estimating simulation parameters
+* Objects for storing those parameters
+* Functions for simulating counts using those parameters
+* Functions for comparing simulations and real datasets
+
+Splatter is built on top of [`scater`][scater] and stores simulations in
+`SCESet` objects. Splatter also has functions for comparing simulations and real
+datasets.
+
+**!Please note!** This site provides documentation for the development version
+of Splatter. For details on the current release please refer to
+https://bioconductor.org/packages/splatter.
+
+## Installation.
+
+### Release version
+
+Splatter has been accepted into the latest version of [Bioconductor][bioc]
+and hence requires the latest version of R (>=3.4).
+
+If you have these installed Splatter can be installed from Bioconductor using
+`biocLite`:
+
+```{r}
+source("https://bioconductor.org/biocLite.R")
+biocLite("splatter")
+```
+
+If you wish to build a local version of the vignette use:
+
+```{r}
+biocLite("splatter", build_vignettes=TRUE)
+```
+
+This will also build the vignette and install all suggested dependencies (which
+aren't required for core functionality). Building the vignette may sometimes
+fail when run from the command line, if this happens try running the install
+command in RStudio.
+
+### Development version
+
+If you want to try the [development version][deve] this can also be installed
+from Bioconductor:
+
+```{r}
+library(BiocInstaller)
+useDevel()
+biocValid() # checks for out of date packages
+biocLite() # (optional) updates out of date packages
+biocLite("splatter")
+```
+
+Depending on the current release cycle you may also need to install the
+development version of R. See [here][bioc-install] for more details.
+
+Alternatively the development version can be installed directly from
+[Github][github]:
+
+```{r}
+devtools::install("Oshlack/splatter")
+```
+
+[scater]: https://github.com/davismcc/scater
+[bioc]: https://bioconductor.org/packages/splatter
+[devel]: https://bioconductor.org/packages/devel/bioc/html/splatter.html
+[bioc-install]: https://www.bioconductor.org/developers/how-to/useDevel/
+[github]: https://github.com/Oshlack/splatter
--
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