diff --git a/DESCRIPTION b/DESCRIPTION
index 466ea86647ab53406edd67c730dfd21f5452b752..0a1aa0a5a98d3bf4b6118fef644f26377cea744c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,7 +21,6 @@ License: GPL-3 + file LICENSE
 LazyData: TRUE
 Depends:
     R (>= 3.4),
-    scater,
     SingleCellExperiment
 Imports:
     akima,
@@ -35,6 +34,7 @@ Imports:
     matrixStats,
     methods,
     scales,
+    scater (>= 1.7.4),
     stats,
     SummarizedExperiment,
     utils
diff --git a/NAMESPACE b/NAMESPACE
index 10ec6366eedc40429d531449e2701f3c72a8c7d4..4d1322b0f0d7bbd875eb9cff48ae09572753e305 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(BASiCSEstimate,SCESet)
+S3method(BASiCSEstimate,SingleCellExperiment)
 S3method(BASiCSEstimate,matrix)
 S3method(lun2Estimate,SingleCellExperiment)
 S3method(lun2Estimate,matrix)
diff --git a/R/BASiCS-estimate.R b/R/BASiCS-estimate.R
index e29e6a0e662edc136bc53f1a3bbd78e8704fa469..cfbea4606a91ae41e95c2363fa74de71766d2025 100644
--- a/R/BASiCS-estimate.R
+++ b/R/BASiCS-estimate.R
@@ -2,8 +2,8 @@
 #'
 #' Estimate simulation parameters for the BASiCS simulation from a real dataset.
 #'
-#' @param counts either a counts matrix or an SCESet object containing count
-#'        data to estimate parameters from.
+#' @param counts either a counts matrix or a SingleCellExperiment object
+#'        containing count data to estimate parameters from.
 #' @param spike.info data.frame describing spike-ins with two columns: "Name"
 #'        giving the names of the spike-in features (must match
 #'        \code{rownames(counts)}) and "Input" giving the number of input
@@ -31,7 +31,10 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
 #'                          Input = rnorm(10, 500, 200),
 #'                          stringsAsFactors = FALSE)
@@ -49,10 +52,12 @@ BASiCSEstimate <- function(counts, spike.info = NULL, batch = NULL,
 
 #' @rdname BASiCSEstimate
 #' @export
-BASiCSEstimate.SCESet <- function(counts, spike.info = NULL, batch = NULL,
-                                  n = 20000, thin = 10, burn = 5000,
-                                  params = newBASiCSParams(), verbose = TRUE,
-                                  progress = TRUE, ...) {
+BASiCSEstimate.SingleCellExperiment <- function(counts, spike.info = NULL,
+                                                batch = NULL, n = 20000,
+                                                thin = 10, burn = 5000,
+                                                params = newBASiCSParams(),
+                                                verbose = TRUE, progress = TRUE,
+                                                ...) {
     counts <- BiocGenerics::counts(counts)
     BASiCSEstimate(counts, params)
 }
diff --git a/R/BASiCS-simulate.R b/R/BASiCS-simulate.R
index 78dfa9d47dda34d345a29733daa6c841cbb0e4b7..b8fc8a79e77d40672d0c9007d97474148b7e8c09 100644
--- a/R/BASiCS-simulate.R
+++ b/R/BASiCS-simulate.R
@@ -10,8 +10,8 @@
 #' @details
 #' This function is just a wrapper around \code{\link[BASiCS]{BASiCS_Sim}} that
 #' takes a \code{\link{BASiCSParams}}, runs the simulation then converts the
-#' output to an \code{\link[scater]{SCESet}} object. See
-#' \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
+#' output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+#' See \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
 #' works.
 #'
 #' @return SingleCellExperiment containing simulated counts
diff --git a/R/BASiCSParams-methods.R b/R/BASiCSParams-methods.R
index 90243b242b89972c980b1294ef23f4c78ba5a060..55bc5de268c8f7f6794e7608205c8b28bb7f884f 100644
--- a/R/BASiCSParams-methods.R
+++ b/R/BASiCSParams-methods.R
@@ -68,7 +68,7 @@ setValidity("BASiCSParams", function(object) {
 })
 
 #' @rdname setParam
-setMethod("setParam", "BASiCSParams",function(object, name, value) {
+setMethod("setParam", "BASiCSParams", function(object, name, value) {
     checkmate::assertString(name)
 
     if (name == "nCells" || name == "nBatches") {
diff --git a/R/compare.R b/R/compare.R
index fb1f270dd6a74bc2e71f750fcf4eaa8a0ecfa25e..3743e64e657dbdb05ce5e11c8af874655f977436 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -79,8 +79,8 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
         sce <- addFeatureStats(sce, "counts")
         sce <- addFeatureStats(sce, "cpm")
         sce <- addFeatureStats(sce, "cpm", log = TRUE)
-        colData(sce)$PctZero <- 100 * (1 - colData(sce)$total_features /
-                                           nrow(sce))
+        n.features <- colData(sce)$total_features_by_counts
+        colData(sce)$PctZero <- 100 * (1 - n.features / nrow(sce))
         sces[[name]] <- sce
     }
 
@@ -140,7 +140,7 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
         theme_minimal()
 
     z.gene <- ggplot(features,
-                     aes_string(x = "Dataset", y = "pct_dropout_counts",
+                     aes_string(x = "Dataset", y = "pct_dropout_by_counts",
                                 colour = "Dataset")) +
         geom_boxplot() +
         scale_y_continuous(limits = c(0, 100)) +
@@ -160,7 +160,8 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
         theme_minimal()
 
     mean.zeros <- ggplot(features,
-                         aes_string(x = "MeanCounts", y = "pct_dropout_counts",
+                         aes_string(x = "MeanCounts",
+                                    y = "pct_dropout_by_counts",
                                     colour = "Dataset", fill = "Dataset")) +
         geom_point(size = point.size, alpha = point.alpha) +
         scale_x_log10(labels = scales::comma) +
@@ -296,7 +297,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
     for (name in names(sces)) {
         sce <- sces[[name]]
         if (!identical(dim(sce), ref.dim)) {
-            stop("SCESets must have the same dimensions")
+            stop("all datasets in 'sces' must have the same dimensions")
         }
         rowData(sce)$Dataset <- name
         colData(sce)$Dataset <- name
@@ -304,8 +305,9 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
         cpm(sce) <- scater::calculateCPM(sce, use_size_factors = FALSE)
         sce <- addFeatureStats(sce, "counts")
         sce <- addFeatureStats(sce, "cpm", log = TRUE)
-        colData(sce)$PctZero <- 100 * (1 - colData(sce)$total_features /
-                                                              nrow(sce))
+        n.features <- colData(sce)$total_features_by_counts
+        colData(sce)$PctZero <- 100 * (1 - n.features / nrow(sce))
+        rowData(sce)$RankCounts <- rank(rowData(sce)$mean_counts)
         sces[[name]] <- sce
     }
 
@@ -314,12 +316,12 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
     ref.means <- sort(rowData(ref.sce)$MeanLogCPM)
     ref.vars <- sort(rowData(ref.sce)$VarLogCPM)
     ref.libs <- sort(colData(ref.sce)$total_counts)
-    ref.z.gene <- sort(rowData(ref.sce)$pct_dropout_counts)
+    ref.z.gene <- sort(rowData(ref.sce)$pct_dropout_by_counts)
     ref.z.cell <- sort(colData(ref.sce)$PctZero)
 
-    ref.rank.ord <- order(rowData(ref.sce)$rank_counts)
+    ref.rank.ord <- order(rowData(ref.sce)$RankCounts)
     ref.vars.rank <- rowData(ref.sce)$VarLogCPM[ref.rank.ord]
-    ref.z.gene.rank <- rowData(ref.sce)$pct_dropout_counts[ref.rank.ord]
+    ref.z.gene.rank <- rowData(ref.sce)$pct_dropout_by_counts[ref.rank.ord]
 
     for (name in names(sces)) {
         sce <- sces[[name]]
@@ -334,8 +336,8 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
         colData(sce)$RankDiffLibSize <- colData(sce)$total_counts -
             colData(sce)$RefRankLibSize
         rowData(sce)$RefRankZeros <- ref.z.gene[rank(
-                                               rowData(sce)$pct_dropout_counts)]
-        rowData(sce)$RankDiffZeros <- rowData(sce)$pct_dropout_counts -
+                                               rowData(sce)$pct_dropout_by_counts)]
+        rowData(sce)$RankDiffZeros <- rowData(sce)$pct_dropout_by_counts -
             rowData(sce)$RefRankZeros
         colData(sce)$RefRankZeros <- ref.z.cell[rank(
                                                colData(sce)$PctZero)]
@@ -343,9 +345,9 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
             colData(sce)$RefRankZeros
 
         rowData(sce)$MeanRankVarDiff <- rowData(sce)$VarLogCPM -
-            ref.vars.rank[rowData(sce)$rank_counts]
-        rowData(sce)$MeanRankZerosDiff <- rowData(sce)$pct_dropout_counts -
-            ref.z.gene.rank[rowData(sce)$rank_counts]
+            ref.vars.rank[rowData(sce)$RankCounts]
+        rowData(sce)$MeanRankZerosDiff <- rowData(sce)$pct_dropout_by_counts -
+            ref.z.gene.rank[rowData(sce)$RankCounts]
 
         sces[[name]] <- sce
     }
@@ -391,7 +393,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
         theme_minimal()
 
     mean.var <- ggplot(features,
-                       aes_string(x = "rank_counts", y = "MeanRankVarDiff",
+                       aes_string(x = "RankCounts", y = "MeanRankVarDiff",
                                   colour = "Dataset", fill = "Dataset")) +
         geom_hline(yintercept = 0, colour = "red") +
         geom_point(size = point.size, alpha = point.alpha) +
@@ -434,7 +436,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
         theme_minimal()
 
     mean.zeros <- ggplot(features,
-                       aes_string(x = "rank_counts", y = "MeanRankZerosDiff",
+                       aes_string(x = "RankCounts", y = "MeanRankZerosDiff",
                                   colour = "Dataset", fill = "Dataset")) +
         geom_hline(yintercept = 0, colour = "red") +
         geom_point(size = point.size, alpha = point.alpha) +
@@ -479,7 +481,8 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
         theme_minimal()
 
     z.gene.qq <- ggplot(features,
-                        aes_string(x = "RefRankZeros", y = "pct_dropout_counts",
+                        aes_string(x = "RefRankZeros",
+                                   y = "pct_dropout_by_counts",
                                    colour = "Dataset")) +
         geom_abline(intercept = 0, slope = 1, colour = "red") +
         geom_point(size = point.size, alpha = point.alpha) +
@@ -714,8 +717,8 @@ makeDiffPanel <- function(diff, title = "Difference comparison",
 #' \dontrun{
 #' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-#' comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
-#' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+#' comparison <- compSCEs(list(Splat = sim1, Simple = sim2))
+#' difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
 #' panel <- makeOverallPanel(comparison, difference)
 #' }
 #'
diff --git a/R/lun-estimate.R b/R/lun-estimate.R
index 3191a5d81b2ae16ce8c902f86faf7371830d1ad8..298c84ba27f35cfb6b09c83c7191ec2434a09735 100644
--- a/R/lun-estimate.R
+++ b/R/lun-estimate.R
@@ -14,7 +14,10 @@
 #' @return LunParams object containing the estimated parameters.
 #'
 #' @examples
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' params <- lunEstimate(sc_example_counts)
 #' params
 #' @export
diff --git a/R/lun2-estimate.R b/R/lun2-estimate.R
index df51b84699291ace5b99df5da81caefd1d8c88c0..f82bf8a75e4af0690d8c1e53e7ef96c0cd88898b 100644
--- a/R/lun2-estimate.R
+++ b/R/lun2-estimate.R
@@ -20,8 +20,11 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
 #' data("sc_example_cell_info")
+#' 
 #' plates <- factor(sc_example_cell_info$Mutation_Status)
 #' params <- lun2Estimate(sc_example_counts, plates, min.size = 20)
 #' params
diff --git a/R/mfa-estimate.R b/R/mfa-estimate.R
index f3abf2f12b4f853fa060a2fdad398be24b077d57..62aa212951ec26e51ad7f7aaea05c27ee585e1d2 100644
--- a/R/mfa-estimate.R
+++ b/R/mfa-estimate.R
@@ -15,7 +15,10 @@
 #' @return MFAParams object containing the estimated parameters.
 #'
 #' @examples
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' params <- mfaEstimate(sc_example_counts)
 #' params
 #' @export
diff --git a/R/pheno-estimate.R b/R/pheno-estimate.R
index 61cf4fc4541fa47916b120a9462338c3d1fa12a9..cccf02fd575db38a2a210602b7f2501a480aee72 100644
--- a/R/pheno-estimate.R
+++ b/R/pheno-estimate.R
@@ -15,7 +15,10 @@
 #' @return PhenoParams object containing the estimated parameters.
 #'
 #' @examples
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' params <- phenoEstimate(sc_example_counts)
 #' params
 #' @export
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index 9c213670a4aec8d72f1c08305aa4c4894e1f3fbb..cb5b2b3e3d4fbf4eef4704de26bf91813f8f1557 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -25,7 +25,10 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
 #' params <- scDDEstimate(sc_example_counts, conditions)
 #' params
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 3a50a4143ad591c6f0ee1790cfedd2f5903b6f3e..1f9e6cc653bbfa215e695d09a2d3268eb7372152 100644
--- a/R/simple-estimate.R
+++ b/R/simple-estimate.R
@@ -16,7 +16,10 @@
 #' @return SimpleParams object containing the estimated parameters.
 #'
 #' @examples
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' params <- simpleEstimate(sc_example_counts)
 #' params
 #' @export
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index ead3c49fe500c4173e69eab9bddb2ccc48ae758f..b1c20ffd753f3efa484a6f303b6a4378603a2ee1 100644
--- a/R/splat-estimate.R
+++ b/R/splat-estimate.R
@@ -16,7 +16,10 @@
 #' @return SplatParams object containing the estimated parameters.
 #'
 #' @examples
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' params <- splatEstimate(sc_example_counts)
 #' params
 #' @export
diff --git a/R/utils.R b/R/utils.R
index 39e770d8932c8bb185df020cbd45fc54bdf5a47a..0a9098758d0d6490b3749452eb1189717b071104 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -23,6 +23,9 @@ logistic <- function(x, x0, k) {
 #'         common columns.
 rbindMatched <- function(df1, df2) {
     common.names <- intersect(colnames(df1), colnames(df2))
+    if (length(common.names) < 2) {
+        stop("There must be at least two columns in common")
+    }
     combined <- rbind(df1[, common.names], df2[, common.names])
 
     return(combined)
diff --git a/R/zinb-estimate.R b/R/zinb-estimate.R
index 2a14443ccba5949f9cfba69730a0887b7b4ecdb3..8af73ab26e3d8a4453fbbe480acdf0c74f600b9c 100644
--- a/R/zinb-estimate.R
+++ b/R/zinb-estimate.R
@@ -29,7 +29,10 @@
 #'
 #' @examples
 #' \dontrun{
+#' # Load example data
+#' library(scater)
 #' data("sc_example_counts")
+#'
 #' params <- zinbEstimate(sc_example_counts)
 #' params
 #' }
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 5a8f3a7499fc3c12f44f98f77d44b9f271916ced..968dea9e3a82260613789c68a3cadfcfd2ca8353 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -47,7 +47,7 @@ reference:
       - '`lun2Simulate`'
       - '`lunSimulate`'
       - '`mfaSimulate`'
-      - '`phenoEstimate`'
+      - '`phenoSimulate`'
       - '`scDDSimulate`'
       - '`simpleSimulate`'
       - '`splatSimBatchCellMeans`'
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index 7cf011b57078dcbeefdc53c607d081e60f065336..6a49094cc0b4d247c8d138ccbc21456c5c6d3160 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="/index.html">
+  <a href="index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -788,7 +788,7 @@ Public License instead of this License.  But first, please read
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 0397c06a5453ca4d43d67d852a1cd9949e45d261..d95fc09b910665f2c12c4fbcc07169eed9bb383a 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -96,7 +96,7 @@
       </header>
 
       <div class="page-header">
-  <h1>Articles <small>version&nbsp;1.1.8</small></h1>
+  <h1>Articles <small>version&nbsp;1.3.1</small></h1>
 </div>
 
 <div class="row">
@@ -118,7 +118,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index e0d8ac2b787a46c2c758fdce42ee98b38aabb6e8..3b44f7e17b71839571e480599ad8f904531add6f 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -39,7 +39,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -76,34 +76,28 @@
       <h1>Introduction to Splatter</h1>
                         <h4 class="author">Luke Zappia</h4>
             
-            <h4 class="date">2017-10-13</h4>
+            <h4 class="date">2018-01-30</h4>
           </div>
 
     
     
 <div class="contents">
-<div class="figure">
-<img src="splatter-logo-small.png" alt="Splatter logo"><p class="caption">Splatter logo</p>
-</div>
-<p>Welcome to Splatter! Splatter is an R package for the simple simulation of single-cell RNA sequencing data. This vignette gives an overview and introduction to Splatter’s functionality.</p>
-<div id="installation" class="section level1">
-<h1 class="hasAnchor">
-<a href="#installation" class="anchor"></a>Installation</h1>
+<figure><img src="splatter-logo-small.png" alt="Splatter logo"><figcaption>Splatter logo</figcaption></figure><p>Welcome to Splatter! Splatter is an R package for the simple simulation of single-cell RNA sequencing data. This vignette gives an overview and introduction to Splatter’s functionality.</p>
+<section id="installation" class="level1"><h1>Installation</h1>
 <p>Splatter can be installed from Bioconductor:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">source</span>(<span class="st">"https://bioconductor.org/biocLite.R"</span>)
-<span class="kw">biocLite</span>(<span class="st">"splatter"</span>)</code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">source</span>(<span class="st">"https://bioconductor.org/biocLite.R"</span>)</a>
+<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">biocLite</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
 <p>To install the most recent development version from Github use:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">biocLite</span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>, 
-         <span class="dt">build_vignettes =</span> <span class="ot">TRUE</span>)</code></pre></div>
-</div>
-<div id="quickstart" class="section level1">
-<h1 class="hasAnchor">
-<a href="#quickstart" class="anchor"></a>Quickstart</h1>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw">biocLite</span>(<span class="st">"Oshlack/splatter"</span>, <span class="dt">dependencies =</span> <span class="ot">TRUE</span>,</a>
+<a class="sourceLine" id="cb2-2" data-line-number="2">         <span class="dt">build_vignettes =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+</section><section id="quickstart" class="level1"><h1>Quickstart</h1>
 <p>Assuming you already have a matrix of count data similar to that you wish to simulate there are two simple steps to creating a simulated data set with Splatter. Here is an example using the example dataset in the <code>scater</code> package:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load package</span>
-<span class="kw">library</span>(splatter)</code></pre></div>
-<pre><code>## Loading required package: scater</code></pre>
-<pre><code>## Loading required package: Biobase</code></pre>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># Load package</span></a>
+<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw">library</span>(splatter)</a></code></pre></div>
+<pre><code>## Loading required package: SingleCellExperiment</code></pre>
+<pre><code>## Loading required package: SummarizedExperiment</code></pre>
+<pre><code>## Loading required package: GenomicRanges</code></pre>
+<pre><code>## Loading required package: stats4</code></pre>
 <pre><code>## Loading required package: BiocGenerics</code></pre>
 <pre><code>## Loading required package: parallel</code></pre>
 <pre><code>## 
@@ -118,23 +112,14 @@
 ##     IQR, mad, sd, var, xtabs</code></pre>
 <pre><code>## The following objects are masked from 'package:base':
 ## 
-##     anyDuplicated, append, as.data.frame, cbind, colMeans,
-##     colnames, colSums, do.call, duplicated, eval, evalq, Filter,
-##     Find, get, grep, grepl, intersect, is.unsorted, lapply,
-##     lengths, Map, mapply, match, mget, order, paste, pmax,
-##     pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
-##     rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
-##     tapply, union, unique, unsplit, which, which.max, which.min</code></pre>
-<pre><code>## Welcome to Bioconductor
-## 
-##     Vignettes contain introductory material; view with
-##     'browseVignettes()'. To cite Bioconductor, see
-##     'citation("Biobase")', and for packages 'citation("pkgname")'.</code></pre>
-<pre><code>## Loading required package: ggplot2</code></pre>
-<pre><code>## Loading required package: SingleCellExperiment</code></pre>
-<pre><code>## Loading required package: SummarizedExperiment</code></pre>
-<pre><code>## Loading required package: GenomicRanges</code></pre>
-<pre><code>## Loading required package: stats4</code></pre>
+##     anyDuplicated, append, as.data.frame, basename, cbind,
+##     colMeans, colnames, colSums, dirname, do.call, duplicated,
+##     eval, evalq, Filter, Find, get, grep, grepl, intersect,
+##     is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
+##     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
+##     Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
+##     table, tapply, union, unique, unsplit, which, which.max,
+##     which.min</code></pre>
 <pre><code>## Loading required package: S4Vectors</code></pre>
 <pre><code>## 
 ## Attaching package: 'S4Vectors'</code></pre>
@@ -143,6 +128,12 @@
 ##     expand.grid</code></pre>
 <pre><code>## Loading required package: IRanges</code></pre>
 <pre><code>## Loading required package: GenomeInfoDb</code></pre>
+<pre><code>## Loading required package: Biobase</code></pre>
+<pre><code>## Welcome to Bioconductor
+## 
+##     Vignettes contain introductory material; view with
+##     'browseVignettes()'. To cite Bioconductor, see
+##     'citation("Biobase")', and for packages 'citation("pkgname")'.</code></pre>
 <pre><code>## Loading required package: DelayedArray</code></pre>
 <pre><code>## Loading required package: matrixStats</code></pre>
 <pre><code>## 
@@ -150,14 +141,18 @@
 <pre><code>## The following objects are masked from 'package:Biobase':
 ## 
 ##     anyMissing, rowMedians</code></pre>
+<pre><code>## Loading required package: BiocParallel</code></pre>
 <pre><code>## 
 ## Attaching package: 'DelayedArray'</code></pre>
 <pre><code>## The following objects are masked from 'package:matrixStats':
 ## 
 ##     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges</code></pre>
-<pre><code>## The following object is masked from 'package:base':
+<pre><code>## The following objects are masked from 'package:base':
 ## 
-##     apply</code></pre>
+##     aperm, apply</code></pre>
+<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1"><span class="co"># Load example data</span></a>
+<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw">library</span>(scater)</a></code></pre></div>
+<pre><code>## Loading required package: ggplot2</code></pre>
 <pre><code>## 
 ## Attaching package: 'scater'</code></pre>
 <pre><code>## The following object is masked from 'package:S4Vectors':
@@ -166,12 +161,11 @@
 <pre><code>## The following object is masked from 'package:stats':
 ## 
 ##     filter</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load example data</span>
-<span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)
-<span class="co"># Estimate parameters from example data</span>
-params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)
-<span class="co"># Simulate data using estimated parameters</span>
-sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">dropout.present =</span> <span class="ot">FALSE</span>)</code></pre></div>
+<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1"><span class="kw">data</span>(<span class="st">"sc_example_counts"</span>)</a>
+<a class="sourceLine" id="cb34-2" data-line-number="2"><span class="co"># Estimate parameters from example data</span></a>
+<a class="sourceLine" id="cb34-3" data-line-number="3">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a>
+<a class="sourceLine" id="cb34-4" data-line-number="4"><span class="co"># Simulate data using estimated parameters</span></a>
+<a class="sourceLine" id="cb34-5" data-line-number="5">sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">dropout.present =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## Getting parameters...</code></pre>
 <pre><code>## Creating simulation object...</code></pre>
 <pre><code>## Simulating library sizes...</code></pre>
@@ -181,15 +175,10 @@ sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSi
 <pre><code>## Simulating dropout (if needed)...</code></pre>
 <pre><code>## Done!</code></pre>
 <p>These steps will be explained in detail in the following sections but briefly the first step takes a dataset and estimates simulation parameters from it and the second step takes those parameters and simulates a new dataset.</p>
-</div>
-<div id="the-splat-simulation" class="section level1">
-<h1 class="hasAnchor">
-<a href="#the-splat-simulation" class="anchor"></a>The Splat simulation</h1>
+</section><section id="the-splat-simulation" class="level1"><h1>The Splat simulation</h1>
 <p>Before we look at how we estimate parameters let’s first look at how Splatter simulates data and what those parameters are. We use the term ‘Splat’ to refer to the Splatter’s own simulation and differentiate it from the package itself. The core of the Splat model is a gamma-Poisson distribution used to generate a gene by cell matrix of counts. Mean expression levels for each gene are simulated from a <a href="https://en.wikipedia.org/wiki/Gamma_distribution">gamma distribution</a> and the Biological Coefficient of Variation is used to enforce a mean-variance trend before counts are simulated from a <a href="https://en.wikipedia.org/wiki/Poisson_distribution">Poisson distribution</a>. Splat also allows you to simulate expression outlier genes (genes with mean expression outside the gamma distribution) and dropout (random knock out of counts based on mean expression). Each cell is given an expected library size (simulated from a log-normal distribution) that makes it easier to match to a given dataset.</p>
 <p>Splat can also simulate differential expression between groups of different types of cells or differentiation paths between different cells types where expression changes in a continuous way. These are described further in the <a href="#simulating-counts">simulating counts</a> section.</p>
-<div id="parameters" class="section level2">
-<h2 class="hasAnchor">
-<a href="#parameters" class="anchor"></a>Parameters</h2>
+<section id="parameters" class="level2"><h2>Parameters</h2>
 <p>The parameters required for the Splat simulation are briefly described here:</p>
 <ul>
 <li>
@@ -304,20 +293,16 @@ sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSi
 </li>
 </ul>
 <p>While this may look like a lot of parameters Splatter attempts to make it easy for the user, both by providing sensible defaults and making it easy to estimate many of the parameters from real data. For more details on the parameters see <code><a href="../reference/SplatParams.html">?SplatParams</a></code>.</p>
-</div>
-</div>
-<div id="the-splatparams-object" class="section level1">
-<h1 class="hasAnchor">
-<a href="#the-splatparams-object" class="anchor"></a>The <code>SplatParams</code> object</h1>
+</section></section><section id="the-splatparams-object" class="level1"><h1>The <code>SplatParams</code> object</h1>
 <p>All the parameters for the Splat simulation are stored in a <code>SplatParams</code> object. Let’s create a new one and see what it looks like.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()
-params</code></pre></div>
+<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>()</a>
+<a class="sourceLine" id="cb43-2" data-line-number="2">params</a></code></pre></div>
 <pre><code>## A Params object of class SplatParams 
 ## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. 
 ## 
 ## Global: 
 ## (Genes)  (Cells)   [Seed]  
-##   10000      100   237407  
+##   10000      100   253576  
 ## 
 ## 27 additional parameters 
 ## 
@@ -359,21 +344,19 @@ params</code></pre></div>
 ## [Sigma Factor]  
 ##            0.8</code></pre>
 <p>As well as telling us what type of object we have (“A <code>Params</code> object of class <code>SplatParams</code>”) and showing us the values of the parameter this output gives us some extra information. We can see which parameters can be estimated by the <code>splatEstimate</code> function (those in parentheses), which can’t be estimated (those in brackets) and which have been changed from their default values (those in ALL CAPS).</p>
-<div id="getting-and-setting" class="section level2">
-<h2 class="hasAnchor">
-<a href="#getting-and-setting" class="anchor"></a>Getting and setting</h2>
+<section id="getting-and-setting" class="level2"><h2>Getting and setting</h2>
 <p>If we want to look at a particular parameter, for example the number of genes to simulate, we can extract it using the <code>getParam</code> function:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</code></pre></div>
+<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
 <pre><code>## [1] 10000</code></pre>
 <p>Alternatively, to give a parameter a new value we can use the <code>setParam</code> function:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)
-<span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</code></pre></div>
+<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/setParam.html">setParam</a></span>(params, <span class="st">"nGenes"</span>, <span class="dv">5000</span>)</a>
+<a class="sourceLine" id="cb47-2" data-line-number="2"><span class="kw"><a href="../reference/getParam.html">getParam</a></span>(params, <span class="st">"nGenes"</span>)</a></code></pre></div>
 <pre><code>## [1] 5000</code></pre>
 <p>If we want to extract multiple parameters (as a list) or set multiple parameters we can use the <code>getParams</code> or <code>setParams</code> functions:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Set multiple parameters at once (using a list)</span>
-params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw">list</span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))
-<span class="co"># Extract multiple parameters as a list</span>
-<span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</code></pre></div>
+<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using a list)</span></a>
+<a class="sourceLine" id="cb49-2" data-line-number="2">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">update =</span> <span class="kw">list</span>(<span class="dt">nGenes =</span> <span class="dv">8000</span>, <span class="dt">mean.rate =</span> <span class="fl">0.5</span>))</a>
+<a class="sourceLine" id="cb49-3" data-line-number="3"><span class="co"># Extract multiple parameters as a list</span></a>
+<a class="sourceLine" id="cb49-4" data-line-number="4"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"nGenes"</span>, <span class="st">"mean.rate"</span>, <span class="st">"mean.shape"</span>))</a></code></pre></div>
 <pre><code>## $nGenes
 ## [1] 8000
 ## 
@@ -382,15 +365,15 @@ params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/setP
 ## 
 ## $mean.shape
 ## [1] 0.6</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Set multiple parameters at once (using additional arguments)</span>
-params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)
-params</code></pre></div>
+<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" data-line-number="1"><span class="co"># Set multiple parameters at once (using additional arguments)</span></a>
+<a class="sourceLine" id="cb51-2" data-line-number="2">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/setParams.html">setParams</a></span>(params, <span class="dt">mean.shape =</span> <span class="fl">0.5</span>, <span class="dt">de.prob =</span> <span class="fl">0.2</span>)</a>
+<a class="sourceLine" id="cb51-3" data-line-number="3">params</a></code></pre></div>
 <pre><code>## A Params object of class SplatParams 
 ## Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. 
 ## 
 ## Global: 
 ## (GENES)  (Cells)   [Seed]  
-##    8000      100   237407  
+##    8000      100   253576  
 ## 
 ## 27 additional parameters 
 ## 
@@ -433,38 +416,34 @@ params</code></pre></div>
 ##            0.8</code></pre>
 <p>The parameters with have changed are now shown in ALL CAPS to indicate that they been changed form the default.</p>
 <p>We can also set parameters directly when we call <code>newSplatParams</code>:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)
-<span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</code></pre></div>
+<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/newParams.html">newSplatParams</a></span>(<span class="dt">lib.loc =</span> <span class="dv">12</span>, <span class="dt">lib.scale =</span> <span class="fl">0.6</span>)</a>
+<a class="sourceLine" id="cb53-2" data-line-number="2"><span class="kw"><a href="../reference/getParams.html">getParams</a></span>(params, <span class="kw">c</span>(<span class="st">"lib.loc"</span>, <span class="st">"lib.scale"</span>))</a></code></pre></div>
 <pre><code>## $lib.loc
 ## [1] 12
 ## 
 ## $lib.scale
 ## [1] 0.6</code></pre>
-</div>
-</div>
-<div id="estimating-parameters" class="section level1">
-<h1 class="hasAnchor">
-<a href="#estimating-parameters" class="anchor"></a>Estimating parameters</h1>
+</section></section><section id="estimating-parameters" class="level1"><h1>Estimating parameters</h1>
 <p>Splat allows you to estimate many of it’s parameters from a data set containing counts using the <code>splatEstimate</code> function.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Check that sc_example counts is an integer matrix</span>
-<span class="kw">class</span>(sc_example_counts)</code></pre></div>
+<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1"><span class="co"># Check that sc_example counts is an integer matrix</span></a>
+<a class="sourceLine" id="cb55-2" data-line-number="2"><span class="kw">class</span>(sc_example_counts)</a></code></pre></div>
 <pre><code>## [1] "matrix"</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">typeof</span>(sc_example_counts)</code></pre></div>
+<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" data-line-number="1"><span class="kw">typeof</span>(sc_example_counts)</a></code></pre></div>
 <pre><code>## [1] "integer"</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span>
-<span class="kw">dim</span>(sc_example_counts)</code></pre></div>
+<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="co"># Check the dimensions, each row is a gene, each column is a cell</span></a>
+<a class="sourceLine" id="cb59-2" data-line-number="2"><span class="kw">dim</span>(sc_example_counts)</a></code></pre></div>
 <pre><code>## [1] 2000   40</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Show the first few entries</span>
-sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
+<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1"><span class="co"># Show the first few entries</span></a>
+<a class="sourceLine" id="cb61-2" data-line-number="2">sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
 <pre><code>##           Cell_001 Cell_002 Cell_003 Cell_004 Cell_005
 ## Gene_0001        0      123        2        0        0
 ## Gene_0002      575       65        3     1561     2311
 ## Gene_0003        0        0        0        0     1213
 ## Gene_0004        0        1        0        0        0
 ## Gene_0005        0        0       11        0        0</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</code></pre></div>
+<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" data-line-number="1">params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatEstimate.html">splatEstimate</a></span>(sc_example_counts)</a></code></pre></div>
 <p>Here we estimated parameters from a counts matrix but <code>splatEstimate</code> can also take a <code>SingleCellExperiment</code> object. The estimation process has the following steps:</p>
-<ol style="list-style-type: decimal">
+<ol type="1">
 <li>Mean parameters are estimated by fitting a gamma distribution to the mean expression levels.</li>
 <li>Library size parameters are estimated by fitting a log-normal distribution to the library sizes.</li>
 <li>Expression outlier parameters are estimated by determining the number of outliers and fitting a log-normal distribution to their difference from the median.</li>
@@ -472,12 +451,9 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 <li>Dropout parameters are estimated by checking if dropout is present and fitting a logistic function to the relationship between mean expression and proportion of zeros.</li>
 </ol>
 <p>For more details of the estimation procedures see <code><a href="../reference/splatEstimate.html">?splatEstimate</a></code>.</p>
-</div>
-<div id="simulating-counts" class="section level1">
-<h1 class="hasAnchor">
-<a href="#simulating-counts" class="anchor"></a>Simulating counts</h1>
+</section><section id="simulating-counts" class="level1"><h1>Simulating counts</h1>
 <p>Once we have a set of parameters we are happy with we can use <code>splatSimulate</code> to simulate counts. If we want to make small adjustments to the parameters we can provide them as additional arguments, alternatively if we don’t supply any parameters the defaults will be used:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">dropout.present =</span> <span class="ot">FALSE</span>)</code></pre></div>
+<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1">sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(params, <span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">dropout.present =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## Getting parameters...</code></pre>
 <pre><code>## Creating simulation object...</code></pre>
 <pre><code>## Simulating library sizes...</code></pre>
@@ -486,7 +462,7 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 <pre><code>## Simulating counts..</code></pre>
 <pre><code>## Simulating dropout (if needed)...</code></pre>
 <pre><code>## Done!</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim</code></pre></div>
+<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">sim</a></code></pre></div>
 <pre><code>## class: SingleCellExperiment 
 ## dim: 1000 40 
 ## metadata(1): params
@@ -498,53 +474,57 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 ## reducedDimNames(0):
 ## spikeNames(0):</code></pre>
 <p>Looking at the output of <code>splatSimulate</code> we can see that <code>sim</code> is <code>SingleCellExperiment</code> object with 1000 features (genes) and 40 samples (cells). The main part of this object is a features by samples matrix containing the simulated counts (accessed using <code>counts</code>), although it can also hold other expression measures such as FPKM or TPM. Additionaly a <code>SingleCellExperiment</code> contains phenotype information about each cell (accessed using <code>colData</code>) and feature information about each gene (accessed using <code>rowData</code>). Splatter uses these slots, as well as <code>assays</code>, to store information about the intermediate values of the simulation.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Access the counts</span>
-<span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
+<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" data-line-number="1"><span class="co"># Access the counts</span></a>
+<a class="sourceLine" id="cb75-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
 <pre><code>##       Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1   208     2     0     0     0
-## Gene2    48     0     0     0     0
-## Gene3     0     0     0   240     0
-## Gene4     0     0    12   626     0
-## Gene5    58     0    47     0     0</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about genes</span>
-<span class="kw">head</span>(<span class="kw">rowData</span>(sim))</code></pre></div>
+## Gene1    13     0     0     0     0
+## Gene2   322     0    70     0     0
+## Gene3   899     0   109     2     2
+## Gene4     0     0     0     0     0
+## Gene5    11     0     0     0   122</code></pre>
+<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" data-line-number="1"><span class="co"># Information about genes</span></a>
+<a class="sourceLine" id="cb77-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
 <pre><code>## DataFrame with 6 rows and 4 columns
-##       Gene BaseGeneMean OutlierFactor    GeneMean
-##   &lt;factor&gt;    &lt;numeric&gt;     &lt;numeric&gt;   &lt;numeric&gt;
-## 1    Gene1   8.84938916             1  8.84938916
-## 2    Gene2   2.09254274             1  2.09254274
-## 3    Gene3  76.54642638             1 76.54642638
-## 4    Gene4  48.29447650             1 48.29447650
-## 5    Gene5   8.38049805             1  8.38049805
-## 6    Gene6   0.03711706             1  0.03711706</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Information about cells</span>
-<span class="kw">head</span>(<span class="kw">colData</span>(sim))</code></pre></div>
+##       Gene BaseGeneMean OutlierFactor   GeneMean
+##   &lt;factor&gt;    &lt;numeric&gt;     &lt;numeric&gt;  &lt;numeric&gt;
+## 1    Gene1    16.052376             1  16.052376
+## 2    Gene2   239.127600             1 239.127600
+## 3    Gene3    43.214270             1  43.214270
+## 4    Gene4    10.362140             1  10.362140
+## 5    Gene5     5.141514             1   5.141514
+## 6    Gene6    22.376227             1  22.376227</code></pre>
+<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1"><span class="co"># Information about cells</span></a>
+<a class="sourceLine" id="cb79-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
 <pre><code>## DataFrame with 6 rows and 3 columns
 ##           Cell       Batch ExpLibSize
 ##       &lt;factor&gt; &lt;character&gt;  &lt;numeric&gt;
-## Cell1    Cell1      Batch1   369673.5
-## Cell2    Cell2      Batch1   837884.1
-## Cell3    Cell3      Batch1   211900.0
-## Cell4    Cell4      Batch1   469342.1
-## Cell5    Cell5      Batch1   358101.8
-## Cell6    Cell6      Batch1   984061.6</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Gene by cell matrices</span>
-<span class="kw">names</span>(<span class="kw">assays</span>(sim))</code></pre></div>
+## Cell1    Cell1      Batch1   759572.6
+## Cell2    Cell2      Batch1   173250.1
+## Cell3    Cell3      Batch1   173683.2
+## Cell4    Cell4      Batch1   310137.4
+## Cell5    Cell5      Batch1   581948.2
+## Cell6    Cell6      Batch1   191958.7</code></pre>
+<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
+<a class="sourceLine" id="cb81-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
 <pre><code>## [1] "BatchCellMeans" "BaseCellMeans"  "BCV"            "CellMeans"     
 ## [5] "TrueCounts"     "counts"</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Example of cell means matrix</span>
-<span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
-<pre><code>##              Cell1        Cell2        Cell3        Cell4        Cell5
-## Gene1 1.777352e+02 6.087412e-01 6.358857e-17 5.040406e-01 3.086920e-06
-## Gene2 5.735710e+01 8.038331e-06 1.675001e-06 9.275255e-02 5.368496e-08
-## Gene3 1.307104e-03 4.675363e-09 7.657201e-20 2.453874e+02 1.578852e+00
-## Gene4 2.107991e-04 1.060652e-03 1.201788e+01 6.365346e+02 5.394848e-17
-## Gene5 6.441256e+01 8.666657e-05 4.797971e+01 9.699099e-08 8.152520e-15</code></pre>
+<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
+<a class="sourceLine" id="cb83-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<pre><code>##             Cell1        Cell2        Cell3        Cell4        Cell5
+## Gene1   8.5956994 9.648645e-09 7.852996e-03 1.810763e-10 3.232297e-09
+## Gene2 319.0032589 2.952430e-03 6.347924e+01 2.594855e-14 2.017484e-04
+## Gene3 922.5537934 7.184557e-01 9.681238e+01 8.432496e-01 4.545795e+00
+## Gene4   0.0520192 3.720615e-13 1.526374e-05 2.539425e-05 1.324239e-08
+## Gene5  10.6228213 1.550409e-06 6.657368e-01 1.943364e-02 1.079607e+02</code></pre>
 <p>An additional (big) advantage of outputting a <code>SingleCellExperiment</code> is that we get immediate access to other analysis packages, such as the plotting functions in <code>scater</code>. For example we can make a PCA plot:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plotPCA</span>(sim, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
+<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
+<a class="sourceLine" id="cb85-2" data-line-number="2">sim &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
+<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
+<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
+<a class="sourceLine" id="cb87-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plotPCA">plotPCA</a></span>(sim)</a></code></pre></div>
 <p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>(<strong>NOTE:</strong> Your values and plots may look different as the simulation is random and produces different results each time it is run.)</p>
-<p>For more details about the <code>SingleCellExperiment</code> object refer to the <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">vignette</a>. For information about what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
+<p>For more details about the <code>SingleCellExperiment</code> object refer to the [vignette] <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SCE-vignette</a>. For information about what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
 <p>The <code>splatSimulate</code> function outputs the following additional information about the simulation:</p>
 <ul>
 <li>
@@ -594,72 +574,65 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 </li>
 </ul>
 <p>Values that have been added by Splatter are named using <code>UpperCamelCase</code> to separate them from the <code>underscore_naming</code> used by <code>scater</code> and other packages. For more information on the simulation see <code><a href="../reference/splatSimulate.html">?splatSimulate</a></code>.</p>
-<div id="simulating-groups" class="section level2">
-<h2 class="hasAnchor">
-<a href="#simulating-groups" class="anchor"></a>Simulating groups</h2>
+<section id="simulating-groups" class="level2"><h2>Simulating groups</h2>
 <p>So far we have only simulated a single population of cells but often we are interested in investigating a mixed population of cells and looking to see what cell types are present or what differences there are between them. Splatter is able to simulate these situations by changing the <code>method</code> argument Here we are going to simulate two groups, by specifying the <code>group.prob</code> parameter and setting the <code>method</code> parameter to <code>"groups"</code>:</p>
 <p>(<strong>NOTE:</strong> We have also set the <code>verbose</code> argument to <code>FALSE</code> to stop Splatter printing progress messages.)</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,
-                            <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
+<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
+<a class="sourceLine" id="cb88-2" data-line-number="2">                            <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb88-3" data-line-number="3">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
+<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plotPCA">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
 <p><img src="splatter_files/figure-html/groups-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>As we have set both the group probabilites to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilites that sum to 1.</p>
-</div>
-<div id="simulating-paths" class="section level2">
-<h2 class="hasAnchor">
-<a href="#simulating-paths" class="anchor"></a>Simulating paths</h2>
+</section><section id="simulating-paths" class="level2"><h2>Simulating paths</h2>
 <p>The other situation that is often of interest is a differentiation process where one cell type is changing into another. Splatter approximates this process by simulating a series of steps between two groups and randomly assigning each cell to a step. We can create this kind of simulation using the <code>"paths"</code> method.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.paths &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
+<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">sim.paths &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb91-2" data-line-number="2">sim.paths &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
+<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
+<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plotPCA">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
 <p><img src="splatter_files/figure-html/paths-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>Here the colours represent the “step” of each cell or how far along the differentiation path it is. We can see that the cells with dark colours are more similar to the originating cell type and the light coloured cells are closer to the final, differentiated, cell type. By setting additional parameters it is possible to simulate more complex process (for example multiple mature cell types from a single progenitor).</p>
-</div>
-<div id="batch-effects" class="section level2">
-<h2 class="hasAnchor">
-<a href="#batch-effects" class="anchor"></a>Batch effects</h2>
+</section><section id="batch-effects" class="level2"><h2>Batch effects</h2>
 <p>Another factor that is important in the analysis of any sequencing experiment are batch effects, technical variation that is common to a set of samples processed at the same time. We apply batch effects by telling Splatter how many cells are in each batch:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.batches &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>, <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
+<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1">sim.batches &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb94-2" data-line-number="2">sim.batches &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
+<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
+<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plotPCA">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
 <p><img src="splatter_files/figure-html/batches-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>This looks at lot like when we simulated groups and that is because the process is very similar. The difference is that batch effects are applied to all genes, not just those that are differentially expressed, and the effects are usually smaller. By combining groups and batches we can simulate both unwanted variation that we aren’t interested in (batch) and the wanted variation we are looking for (group):</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),
-                            <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-<span class="kw">plotPCA</span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>,
-        <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</code></pre></div>
+<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb97-2" data-line-number="2">                            <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb97-3" data-line-number="3">sim.groups &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
+<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
+<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plotPCA">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>,</a>
+<a class="sourceLine" id="cb99-2" data-line-number="2">        <span class="dt">exprs_values =</span> <span class="st">"counts"</span>)</a></code></pre></div>
 <p><img src="splatter_files/figure-html/batch-groups-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>Here we see that the effects of the group (first component) are stronger than the batch effects (second component) but by adjusting the parameters we could made the batch effects dominate.</p>
-</div>
-<div id="convenience-functions" class="section level2">
-<h2 class="hasAnchor">
-<a href="#convenience-functions" class="anchor"></a>Convenience functions</h2>
+</section><section id="convenience-functions" class="level2"><h2>Convenience functions</h2>
 <p>Each of the Splatter simulation methods has it’s own convenience function. To simulate a single population use <code><a href="../reference/splatSimulate.html">splatSimulateSingle()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "single")</a></code>), to simulate grops use <code><a href="../reference/splatSimulate.html">splatSimulateGroups()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "groups")</a></code>) or to simulate paths use <code><a href="../reference/splatSimulate.html">splatSimulatePaths()</a></code> (equivalent to <code><a href="../reference/splatSimulate.html">splatSimulate(method = "paths")</a></code>).</p>
-</div>
-</div>
-<div id="other-simulations" class="section level1">
-<h1 class="hasAnchor">
-<a href="#other-simulations" class="anchor"></a>Other simulations</h1>
+</section></section><section id="other-simulations" class="level1"><h1>Other simulations</h1>
 <p>As well as it’s own Splat simulation method the Splatter package contains implementations of other single-cell RNA-seq simulations that have been published or wrappers around simulations included in other packages. To see all the available simulations run the <code><a href="../reference/listSims.html">listSims()</a></code> function:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</code></pre></div>
-<pre><code>## Splatter currently contains 11 simulations 
+<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
+<pre><code>## Splatter currently contains 12 simulations 
 ## 
 ## Splat (splat) 
-## DOI:      GitHub:  
+## DOI: 10.1186/s13059-017-1305-0    GitHub: Oshlack/splatter 
 ## The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added. 
 ## 
 ## Splat Single (splatSingle) 
-## DOI:      GitHub:  
+## DOI: 10.1186/s13059-017-1305-0    GitHub: Oshlack/splatter 
 ## The Splat simulation with a single population. 
 ## 
 ## Splat Groups (splatGroups) 
-## DOI:      GitHub:  
+## DOI: 10.1186/s13059-017-1305-0    GitHub: Oshlack/splatter 
 ## The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution. 
 ## 
 ## Splat Paths (splatPaths) 
-## DOI:      GitHub:  
+## DOI: 10.1186/s13059-017-1305-0    GitHub: Oshlack/splatter 
 ## The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways. 
 ## 
 ## Simple (simple) 
-## DOI:      GitHub:  
+## DOI: 10.1186/s13059-017-1305-0    GitHub: Oshlack/splatter 
 ## A simple simulation with gamma means and negative binomial counts. 
 ## 
 ## Lun (lun) 
@@ -667,13 +640,17 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 ## Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes. 
 ## 
 ## Lun 2 (lun2) 
-## DOI: 10.1101/073973   GitHub: MarioniLab/PlateEffects2016 
+## DOI: 10.1093/biostatistics/kxw055     GitHub: MarioniLab/PlateEffects2016 
 ## Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used. 
 ## 
 ## scDD (scDD) 
 ## DOI: 10.1186/s13059-016-1077-y    GitHub: kdkorthauer/scDD 
 ## The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions. 
 ## 
+## BASiCS (BASiCS) 
+## DOI: 10.1371/journal.pcbi.1004333     GitHub: catavallejos/BASiCS 
+## The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects. 
+## 
 ## mfa (mfa) 
 ## DOI: 10.12688/wellcomeopenres.11087.1     GitHub: kieranrcampbell/mfa 
 ## The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout. 
@@ -686,270 +663,261 @@ sc_example_counts[<span class="dv">1</span><span class="op">:</span><span class=
 ## DOI: 10.1101/125112   GitHub: drisso/zinbwave 
 ## The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.</code></pre>
 <p>(or more conveniently for the vignette as a table)</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</code></pre></div>
+<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</a></code></pre></div>
 <table class="table">
 <thead><tr class="header">
-<th align="left">Name</th>
-<th align="left">Prefix</th>
-<th align="left">DOI</th>
-<th align="left">GitHub</th>
-<th align="left">Description</th>
+<th style="text-align: left;">Name</th>
+<th style="text-align: left;">Prefix</th>
+<th style="text-align: left;">DOI</th>
+<th style="text-align: left;">GitHub</th>
+<th style="text-align: left;">Description</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">Splat</td>
-<td align="left">splat</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added.</td>
+<td style="text-align: left;">Splat</td>
+<td style="text-align: left;">splat</td>
+<td style="text-align: left;">10.1186/s13059-017-1305-0</td>
+<td style="text-align: left;">Oshlack/splatter</td>
+<td style="text-align: left;">The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added.</td>
 </tr>
 <tr class="even">
-<td align="left">Splat Single</td>
-<td align="left">splatSingle</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">The Splat simulation with a single population.</td>
+<td style="text-align: left;">Splat Single</td>
+<td style="text-align: left;">splatSingle</td>
+<td style="text-align: left;">10.1186/s13059-017-1305-0</td>
+<td style="text-align: left;">Oshlack/splatter</td>
+<td style="text-align: left;">The Splat simulation with a single population.</td>
 </tr>
 <tr class="odd">
-<td align="left">Splat Groups</td>
-<td align="left">splatGroups</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">The Splat simulation with multiple groups. Each group can have it’s own differential expression probability and fold change distribution.</td>
+<td style="text-align: left;">Splat Groups</td>
+<td style="text-align: left;">splatGroups</td>
+<td style="text-align: left;">10.1186/s13059-017-1305-0</td>
+<td style="text-align: left;">Oshlack/splatter</td>
+<td style="text-align: left;">The Splat simulation with multiple groups. Each group can have it’s own differential expression probability and fold change distribution.</td>
 </tr>
 <tr class="even">
-<td align="left">Splat Paths</td>
-<td align="left">splatPaths</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">The Splat simulation with differentiation paths. Each path can have it’s own length, skew and probability. Genes can change in non-linear ways.</td>
+<td style="text-align: left;">Splat Paths</td>
+<td style="text-align: left;">splatPaths</td>
+<td style="text-align: left;">10.1186/s13059-017-1305-0</td>
+<td style="text-align: left;">Oshlack/splatter</td>
+<td style="text-align: left;">The Splat simulation with differentiation paths. Each path can have it’s own length, skew and probability. Genes can change in non-linear ways.</td>
 </tr>
 <tr class="odd">
-<td align="left">Simple</td>
-<td align="left">simple</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">A simple simulation with gamma means and negative binomial counts.</td>
+<td style="text-align: left;">Simple</td>
+<td style="text-align: left;">simple</td>
+<td style="text-align: left;">10.1186/s13059-017-1305-0</td>
+<td style="text-align: left;">Oshlack/splatter</td>
+<td style="text-align: left;">A simple simulation with gamma means and negative binomial counts.</td>
 </tr>
 <tr class="even">
-<td align="left">Lun</td>
-<td align="left">lun</td>
-<td align="left">10.1186/s13059-016-0947-7</td>
-<td align="left">MarioniLab/Deconvolution2016</td>
-<td align="left">Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.</td>
+<td style="text-align: left;">Lun</td>
+<td style="text-align: left;">lun</td>
+<td style="text-align: left;">10.1186/s13059-016-0947-7</td>
+<td style="text-align: left;">MarioniLab/Deconvolution2016</td>
+<td style="text-align: left;">Gamma distributed means and negative binomial counts. Cells are given a size factor and differential expression can be simulated with fixed fold changes.</td>
 </tr>
 <tr class="odd">
-<td align="left">Lun 2</td>
-<td align="left">lun2</td>
-<td align="left">10.1101/073973</td>
-<td align="left">MarioniLab/PlateEffects2016</td>
-<td align="left">Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.</td>
+<td style="text-align: left;">Lun 2</td>
+<td style="text-align: left;">lun2</td>
+<td style="text-align: left;">10.1093/biostatistics/kxw055</td>
+<td style="text-align: left;">MarioniLab/PlateEffects2016</td>
+<td style="text-align: left;">Negative binomial counts where the means and dispersions have been sampled from a real dataset. The core feature of the Lun 2 simulation is the addition of plate effects. Differential expression can be added between two groups of plates and optionally a zero-inflated negative-binomial can be used.</td>
 </tr>
 <tr class="even">
-<td align="left">scDD</td>
-<td align="left">scDD</td>
-<td align="left">10.1186/s13059-016-1077-y</td>
-<td align="left">kdkorthauer/scDD</td>
-<td align="left">The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</td>
+<td style="text-align: left;">scDD</td>
+<td style="text-align: left;">scDD</td>
+<td style="text-align: left;">10.1186/s13059-016-1077-y</td>
+<td style="text-align: left;">kdkorthauer/scDD</td>
+<td style="text-align: left;">The scDD simulation samples a given dataset and can simulate differentially expressed and differentially distributed genes between two conditions.</td>
 </tr>
 <tr class="odd">
-<td align="left">mfa</td>
-<td align="left">mfa</td>
-<td align="left">10.12688/wellcomeopenres.11087.1</td>
-<td align="left">kieranrcampbell/mfa</td>
-<td align="left">The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</td>
+<td style="text-align: left;">BASiCS</td>
+<td style="text-align: left;">BASiCS</td>
+<td style="text-align: left;">10.1371/journal.pcbi.1004333</td>
+<td style="text-align: left;">catavallejos/BASiCS</td>
+<td style="text-align: left;">The BASiCS simulation is based on a bayesian model used to deconvolve biological and technical variation and includes spike-ins and batch effects.</td>
 </tr>
 <tr class="even">
-<td align="left">PhenoPath</td>
-<td align="left">pheno</td>
-<td align="left">10.1101/159913</td>
-<td align="left">kieranrcampbell/phenopath</td>
-<td align="left">The PhenoPath simulation produces a pseudotime trajectory with different types of genes.</td>
+<td style="text-align: left;">mfa</td>
+<td style="text-align: left;">mfa</td>
+<td style="text-align: left;">10.12688/wellcomeopenres.11087.1</td>
+<td style="text-align: left;">kieranrcampbell/mfa</td>
+<td style="text-align: left;">The mfa simulation produces a bifurcating pseudotime trajectory. This can optionally include genes with transient changes in expression and added dropout.</td>
 </tr>
 <tr class="odd">
-<td align="left">ZINB-WaVE</td>
-<td align="left">zinb</td>
-<td align="left">10.1101/125112</td>
-<td align="left">drisso/zinbwave</td>
-<td align="left">The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.</td>
+<td style="text-align: left;">PhenoPath</td>
+<td style="text-align: left;">pheno</td>
+<td style="text-align: left;">10.1101/159913</td>
+<td style="text-align: left;">kieranrcampbell/phenopath</td>
+<td style="text-align: left;">The PhenoPath simulation produces a pseudotime trajectory with different types of genes.</td>
+</tr>
+<tr class="even">
+<td style="text-align: left;">ZINB-WaVE</td>
+<td style="text-align: left;">zinb</td>
+<td style="text-align: left;">10.1101/125112</td>
+<td style="text-align: left;">drisso/zinbwave</td>
+<td style="text-align: left;">The ZINB-WaVE simulation simulates counts from a sophisticated zero-inflated negative-binomial distribution including cell and gene-level covariates.</td>
 </tr>
 </tbody>
 </table>
 <p>Each simulation has it’s own prefix which gives the name of the functions associated with that simulation. For example the prefix for the simple simulation is <code>simple</code> so it would store it’s parameters in a <code>SimpleParams</code> object that can be created using <code><a href="../reference/newParams.html">newSimpleParams()</a></code> or estimated from real data using <code><a href="../reference/simpleEstimate.html">simpleEstimate()</a></code>. To simulate data using that simulation you would use <code><a href="../reference/simpleSimulate.html">simpleSimulate()</a></code>. Each simulation returns a <code>SingleCellExperiment</code> object with intermediate values similar to that returned by <code><a href="../reference/splatSimulate.html">splatSimulate()</a></code>. For more detailed information on each simulation see the appropriate help page (eg. <code><a href="../reference/simpleSimulate.html">?simpleSimulate</a></code> for information on how the simple simulation works or <code><a href="../reference/lun2Estimate.html">? lun2Estimate</a></code> for details of how the Lun 2 simulation estimates parameters) or refer to the appropriate paper or package.</p>
-</div>
-<div id="other-expression-values" class="section level1">
-<h1 class="hasAnchor">
-<a href="#other-expression-values" class="anchor"></a>Other expression values</h1>
+</section><section id="other-expression-values" class="level1"><h1>Other expression values</h1>
 <p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to a <code>SingleCellExperiment</code> object but they require a length for each gene. The <code>addGeneLengths</code> function can be used to simulate these lengths:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)
-<span class="kw">head</span>(<span class="kw">rowData</span>(sim))</code></pre></div>
+<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1">sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb103-2" data-line-number="2">sim &lt;-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
+<a class="sourceLine" id="cb103-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
 <pre><code>## DataFrame with 6 rows and 3 columns
 ##       Gene   GeneMean    Length
 ##   &lt;factor&gt;  &lt;numeric&gt; &lt;numeric&gt;
-## 1    Gene1 0.11512934      9592
-## 2    Gene2 1.08395798      1260
-## 3    Gene3 0.07297126      7150
-## 4    Gene4 0.52861074      2131
-## 5    Gene5 2.07154719      1787
-## 6    Gene6 1.48581784       885</code></pre>
+## 1    Gene1 4.98592529       510
+## 2    Gene2 0.03299794      5590
+## 3    Gene3 0.03356105      7265
+## 4    Gene4 0.06417636      5095
+## 5    Gene5 0.25296758      5087
+## 6    Gene6 4.33791562      1087</code></pre>
 <p>We can then use <code>scater</code> to calculate TPM:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">tpm</span>(sim) &lt;-<span class="st"> </span><span class="kw">calculateTPM</span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)
-<span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</code></pre></div>
-<pre><code>##            Cell1      Cell2      Cell3      Cell4      Cell5
-## Gene1 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene2 0.06020259 0.00000000 0.05823678 0.00000000 0.11723920
-## Gene3 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
-## Gene4 0.00000000 0.03420037 0.00000000 0.00000000 0.00000000
-## Gene5 0.12734516 0.16313595 0.08212461 0.08100124 0.08266446</code></pre>
+<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw">tpm</span>(sim) &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
+<a class="sourceLine" id="cb105-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<pre><code>##            Cell1      Cell2     Cell3     Cell4    Cell5
+## Gene1 1.91425324 0.59834736 0.4419499 0.3010339 1.168873
+## Gene2 0.00000000 0.01364746 0.0000000 0.0000000 0.000000
+## Gene3 0.00000000 0.00000000 0.0000000 0.0000000 0.000000
+## Gene4 0.00000000 0.00000000 0.0000000 0.0000000 0.000000
+## Gene5 0.01476266 0.00000000 0.0000000 0.0000000 0.000000</code></pre>
 <p>The default method used by <code>addGeneLengths</code> to simulate lengths is to generate values from a log-normal distribution which are then rounded to give an integer length. The parameters for this distribution are based on human protein coding genes but can be adjusted if needed (for example for other species). Alternatively lengths can be sampled from a provided vector (see <code><a href="../reference/addGeneLengths.html">?addGeneLengths</a></code> for details and an example).</p>
-</div>
-<div id="comparing-simulations-and-real-data" class="section level1">
-<h1 class="hasAnchor">
-<a href="#comparing-simulations-and-real-data" class="anchor"></a>Comparing simulations and real data</h1>
+</section><section id="comparing-simulations-and-real-data" class="level1"><h1>Comparing simulations and real data</h1>
 <p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCEs</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SingleCellExperiment</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sim1 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-sim2 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)
-comparison &lt;-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))
-
-<span class="kw">names</span>(comparison)</code></pre></div>
+<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" data-line-number="1">sim1 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb107-2" data-line-number="2">sim2 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb107-3" data-line-number="3">comparison &lt;-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a></code></pre></div>
+<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.
+## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
+<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1"><span class="kw">names</span>(comparison)</a></code></pre></div>
 <pre><code>## [1] "FeatureData" "PhenoData"   "Plots"</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</code></pre></div>
+<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
 <pre><code>## [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes"
 ## [5] "ZerosGene"    "ZerosCell"    "MeanZeros"</code></pre>
 <p>The returned list has three items. The first two are the combined datasets by gene (<code>FeatureData</code>) and by cell (<code>PhenoData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</code></pre></div>
+<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
 <p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,
-       <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features, <span class="dt">colour =</span> Dataset)) <span class="op">+</span>
-<span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</code></pre></div>
+<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
+<a class="sourceLine" id="cb114-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
+<a class="sourceLine" id="cb114-3" data-line-number="3">       <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb114-4" data-line-number="4"><span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</a></code></pre></div>
 <p><img src="splatter_files/figure-html/comparison-libsize-features-1.png" width="576" style="display: block; margin: auto;"></p>
-<div id="comparing-differences" class="section level2">
-<h2 class="hasAnchor">
-<a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
+<section id="comparing-differences" class="level2"><h2>Comparing differences</h2>
 <p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">difference &lt;-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)
-difference<span class="op">$</span>Plots<span class="op">$</span>Means</code></pre></div>
+<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" data-line-number="1">difference &lt;-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a></code></pre></div>
+<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.
+## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
+<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
 <p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
 <p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</code></pre></div>
+<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
 <p><img src="splatter_files/figure-html/difference-qq-1.png" width="576" style="display: block; margin: auto;"></p>
-</div>
-<div id="making-panels" class="section level2">
-<h2 class="hasAnchor">
-<a href="#making-panels" class="anchor"></a>Making panels</h2>
+</section><section id="making-panels" class="level2"><h2>Making panels</h2>
 <p>Each of these comparisons makes several plots which can be a lot to look at. To make this easier, or to produce figures for publications, you can make use of the functions <code>makeCompPanel</code>, <code>makeDiffPanel</code> and <code>makeOverallPanel</code>.</p>
 <p>These functions combine the plots into a single panel using the <code>cowplot</code> package. The panels can be quite large and hard to view (for example in RStudio’s plot viewer) so it can be better to output the panels and view them separately. Luckily <code>cowplot</code> provides a convenient function for saving the images. Here are some suggested parameters for outputting each of the panels:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># This code is just an example and is not run</span>
-panel &lt;-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)
-cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)
-
-panel &lt;-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)
-cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)
-
-panel &lt;-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)
-cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</code></pre></div>
-</div>
-</div>
-<div id="citing-splatter" class="section level1">
-<h1 class="hasAnchor">
-<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h1>
+<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
+<a class="sourceLine" id="cb119-2" data-line-number="2">panel &lt;-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
+<a class="sourceLine" id="cb119-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb119-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb119-5" data-line-number="5">panel &lt;-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
+<a class="sourceLine" id="cb119-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
+<a class="sourceLine" id="cb119-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb119-8" data-line-number="8">panel &lt;-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
+<a class="sourceLine" id="cb119-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
+</section></section><section id="citing-splatter" class="level1"><h1>Citing Splatter</h1>
 <p>If you use Splatter in your work please cite our paper:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</code></pre></div>
+<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
 <pre><code>## 
-##   Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of
-##   Single-Cell RNA Sequencing Data. bioRxiv. 2017;
-##   doi:10.1101/133173
+##   Zappia L, Phipson B, Oshlack A. Splatter: Simulation of
+##   single-cell RNA sequencing data. Genome Biology. 2017;
+##   doi:10.1186/s13059-017-1305-0
 ## 
 ## A BibTeX entry for LaTeX users is
 ## 
 ##   @Article{,
 ##     author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
-##     title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
-##     journal = {bioRxiv},
+##     title = {Splatter: simulation of single-cell RNA sequencing data},
+##     journal = {Genome Biology},
 ##     year = {2017},
-##     url = {http://dx.doi.org/10.1101/133173},
-##     doi = {10.1101/133173},
+##     url = {http://dx.doi.org/10.1186/s13059-017-1305-0},
+##     doi = {10.1186/s13059-017-1305-0},
 ##   }</code></pre>
-</div>
-<div id="session-information" class="section level1 unnumbered">
-<h1 class="hasAnchor">
-<a href="#session-information" class="anchor"></a>Session information</h1>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">sessionInfo</span>()</code></pre></div>
-<pre><code>## R version 3.4.2 (2017-09-28)
-## Platform: x86_64-apple-darwin15.6.0 (64-bit)
+</section><section id="session-information" class="level1 unnumbered"><h1>Session information</h1>
+<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
+<pre><code>## R Under development (unstable) (2018-01-28 r74177)
+## Platform: x86_64-apple-darwin16.7.0 (64-bit)
 ## Running under: macOS Sierra 10.12.6
 ## 
 ## Matrix products: default
-## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
-## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
+## BLAS: /Users/luke.zappia/r-devel/lib/R/lib/libRblas.dylib
+## LAPACK: /Users/luke.zappia/r-devel/lib/R/lib/libRlapack.dylib
 ## 
 ## locale:
 ## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
 ## 
 ## attached base packages:
-## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
+## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
 ## [8] methods   base     
 ## 
 ## other attached packages:
-##  [1] splatter_1.1.7              scater_1.5.16              
-##  [3] SingleCellExperiment_0.99.4 SummarizedExperiment_1.7.10
-##  [5] DelayedArray_0.3.21         matrixStats_0.52.2         
-##  [7] GenomicRanges_1.29.15       GenomeInfoDb_1.13.5        
-##  [9] IRanges_2.11.19             S4Vectors_0.15.12          
-## [11] ggplot2_2.2.1               Biobase_2.37.2             
-## [13] BiocGenerics_0.23.3        
+##  [1] scater_1.7.4                ggplot2_2.2.1              
+##  [3] splatter_1.3.1              SingleCellExperiment_1.1.2 
+##  [5] SummarizedExperiment_1.9.12 DelayedArray_0.5.17        
+##  [7] BiocParallel_1.13.1         matrixStats_0.53.0         
+##  [9] Biobase_2.39.2              GenomicRanges_1.31.12      
+## [11] GenomeInfoDb_1.15.2         IRanges_2.13.16            
+## [13] S4Vectors_0.17.28           BiocGenerics_0.25.1        
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] bitops_1.0-6            bit64_0.9-7            
-##  [3] progress_1.1.2          rprojroot_1.2          
-##  [5] zinbwave_0.99.9         numDeriv_2016.8-1      
-##  [7] tools_3.4.2             backports_1.1.1        
-##  [9] R6_2.2.2                vipor_0.4.5            
-## [11] DBI_0.7                 lazyeval_0.2.0         
-## [13] colorspace_1.3-2        sp_1.2-5               
-## [15] gridExtra_2.3           prettyunits_1.0.2      
-## [17] bit_1.1-12              compiler_3.4.2         
-## [19] glmnet_2.0-13           pspline_1.0-18         
-## [21] labeling_0.3            scales_0.5.0           
-## [23] checkmate_1.8.4         mvtnorm_1.0-6          
-## [25] stringr_1.2.0           digest_0.6.12          
-## [27] rmarkdown_1.6           XVector_0.17.1         
-## [29] pkgconfig_2.0.1         htmltools_0.3.6        
-## [31] akima_0.6-2             highr_0.6              
-## [33] stabledist_0.7-1        ADGofTest_0.3          
-## [35] limma_3.33.14           rlang_0.1.2.9000       
-## [37] RSQLite_2.0             shiny_1.0.5            
-## [39] bindr_0.1               BiocParallel_1.11.11   
-## [41] dplyr_0.7.4             RCurl_1.95-4.8         
-## [43] magrittr_1.5            GenomeInfoDbData_0.99.1
-## [45] Matrix_1.2-11           Rcpp_0.12.13           
-## [47] ggbeeswarm_0.6.0        munsell_0.4.3          
-## [49] viridis_0.4.0           stringi_1.1.5          
-## [51] yaml_2.1.14             edgeR_3.19.7           
-## [53] MASS_7.3-47             zlibbioc_1.23.0        
-## [55] rhdf5_2.21.6            plyr_1.8.4             
-## [57] grid_3.4.2              blob_1.1.0             
-## [59] shinydashboard_0.6.1    lattice_0.20-35        
-## [61] cowplot_0.8.0           splines_3.4.2          
-## [63] locfit_1.5-9.1          knitr_1.17             
-## [65] rjson_0.2.15            softImpute_1.4         
-## [67] codetools_0.2-15        reshape2_1.4.2         
-## [69] biomaRt_2.33.4          XML_3.98-1.9           
-## [71] glue_1.1.1              evaluate_0.10.1        
-## [73] data.table_1.10.4-2     httpuv_1.3.5           
-## [75] foreach_1.4.3           gtable_0.2.0           
-## [77] assertthat_0.2.0        mime_0.5               
-## [79] xtable_1.8-2            survival_2.41-3        
-## [81] pcaPP_1.9-72            viridisLite_0.2.0      
-## [83] gsl_1.9-10.3            tibble_1.3.4           
-## [85] copula_0.999-18         iterators_1.0.8        
-## [87] AnnotationDbi_1.39.4    beeswarm_0.2.3         
-## [89] memoise_1.1.0           tximport_1.5.1         
-## [91] bindrcpp_0.2            fitdistrplus_1.0-9</code></pre>
-</div>
+##  [1] bitops_1.0-6             bit64_0.9-7             
+##  [3] progress_1.1.2           httr_1.3.1              
+##  [5] rprojroot_1.3-2          tools_3.5.0             
+##  [7] backports_1.1.2          R6_2.2.2                
+##  [9] vipor_0.4.5              DBI_0.7                 
+## [11] lazyeval_0.2.1           colorspace_1.3-2        
+## [13] sp_1.2-7                 gridExtra_2.3           
+## [15] prettyunits_1.0.2        bit_1.1-12              
+## [17] compiler_3.5.0           labeling_0.3            
+## [19] scales_0.5.0             checkmate_1.8.5         
+## [21] stringr_1.2.0            digest_0.6.15           
+## [23] rmarkdown_1.8            XVector_0.19.8          
+## [25] pkgconfig_2.0.1          htmltools_0.3.6         
+## [27] akima_0.6-2              highr_0.6               
+## [29] limma_3.35.6             rlang_0.1.6.9003        
+## [31] RSQLite_2.0              shiny_1.0.5             
+## [33] DelayedMatrixStats_1.1.8 bindr_0.1               
+## [35] dplyr_0.7.4              RCurl_1.95-4.10         
+## [37] magrittr_1.5             GenomeInfoDbData_1.1.0  
+## [39] Matrix_1.2-12            Rcpp_0.12.15            
+## [41] ggbeeswarm_0.6.0         munsell_0.4.3           
+## [43] Rhdf5lib_1.1.5           viridis_0.4.1           
+## [45] stringi_1.1.6            yaml_2.1.16             
+## [47] edgeR_3.21.6             MASS_7.3-48             
+## [49] zlibbioc_1.25.0          rhdf5_2.23.5            
+## [51] plyr_1.8.4               grid_3.5.0              
+## [53] blob_1.1.0               shinydashboard_0.6.1    
+## [55] lattice_0.20-35          cowplot_0.9.2           
+## [57] splines_3.5.0            locfit_1.5-9.1          
+## [59] knitr_1.19               pillar_1.1.0            
+## [61] rjson_0.2.15             reshape2_1.4.3          
+## [63] biomaRt_2.35.10          XML_3.98-1.9            
+## [65] glue_1.2.0               evaluate_0.10.1         
+## [67] data.table_1.10.4-3      httpuv_1.3.5            
+## [69] gtable_0.2.0             assertthat_0.2.0        
+## [71] mime_0.5                 xtable_1.8-2            
+## [73] survival_2.41-3          viridisLite_0.2.0       
+## [75] tibble_1.4.2             AnnotationDbi_1.41.4    
+## [77] beeswarm_0.2.3           memoise_1.1.0           
+## [79] tximport_1.7.4           bindrcpp_0.2            
+## [81] fitdistrplus_1.0-9</code></pre>
+</section>
 </div>
   </div>
 
@@ -1001,7 +969,7 @@ cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumenta
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
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index 52fbe4076f3918a4d4da00ca7aa5af3e47dd9159..28822b274997cbdfbbd523d66f299a930fd7cdec 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="/index.html">
+  <a href="index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ doi: <a href="http://doi.org/10.1186/s13059-017-1305-0">10.1186/s13059-017-1305-
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/index.html b/docs/index.html
index a0cd79fa1741025aee2fc52ee0ad95dc3e664daa..c87b1af22b8e0e28db391daf1adee22d9afc75f9 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -39,7 +39,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
-  <a href="/index.html">
+  <a href="index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -82,14 +82,10 @@
 <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>Splatter is built on top of <a href="https://github.com/davismcc/scater"><code>scater</code></a> and stores simulations in <a href="https://github.com/drisso/SingleCellExperiment"><code>SingleCellExperiment</code></a> 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="release-version" class="section level3">
-<h3 class="hasAnchor">
-<a href="#release-version" class="anchor"></a>Release version</h3>
+<section class="level2"><h2>Installation.</h2>
+<section class="level3"><h3>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 (&gt;=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")
@@ -97,10 +93,7 @@ biocLite("splatter")</code></pre>
 <p>If you wish to build a local version of the vignette use:</p>
 <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 id="development-version" class="section level3">
-<h3 class="hasAnchor">
-<a href="#development-version" class="anchor"></a>Development version</h3>
+</section><section class="level3"><h3>Development version</h3>
 <p>If you want to try the <a href="https://bioconductor.org/packages/devel/bioc/html/splatter.html">development version</a> this can also be installed from Bioconductor:</p>
 <pre class="{r}"><code>library(BiocInstaller)
 useDevel()
@@ -110,10 +103,8 @@ 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>
+</section></section>
 </div>
-</div>
-
-  </div>
 
   <div class="col-md-3" id="sidebar">
     <h2>Links</h2>
@@ -155,7 +146,7 @@ biocLite("splatter")</code></pre>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/news/index.html b/docs/news/index.html
index 71c2603f53a2ef7fe5e51a7df7e83990cc71029b..791dca4dfac1b5349430e71c784bee702e951aad 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -103,353 +103,6 @@
     </div>
 
     <div class="contents">
-    <div id="version-1-1-8-2017-10-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-8-2017-10-13" class="anchor"></a>Version 1.1.8 (2017-10-13)</h2>
-<ul>
-<li>Add BASiCS simulation</li>
-<li>Update Splatter citation</li>
-<li>Update Lun2 reference</li>
-</ul>
-</div>
-    <div id="version-1-1-7-2017-10-05" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-7-2017-10-05" class="anchor"></a>Version 1.1.7 (2017-10-05)</h2>
-<ul>
-<li>Add PhenoPath simulation</li>
-<li>Add ZINB-WaVE simulation</li>
-<li>Adjust mfaSimulate output</li>
-</ul>
-</div>
-    <div id="version-1-1-6-2017-10-02" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-6-2017-10-02" class="anchor"></a>Version 1.1.6 (2017-10-02)</h2>
-<ul>
-<li>Update scDD version</li>
-<li>Add mfa simulation</li>
-</ul>
-</div>
-    <div id="version-1-1-5-2017-09-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-5-2017-09-13" class="anchor"></a>Version 1.1.5 (2017-09-13)</h2>
-<ul>
-<li>Convert to SingleCellExperiment</li>
-</ul>
-</div>
-    <div id="version-1-1-4-2017-08-04" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-4-2017-08-04" class="anchor"></a>Version 1.1.4 (2017-08-04)</h2>
-<ul>
-<li>Fix group factors bug</li>
-</ul>
-</div>
-    <div id="version-1-1-3-2017-07-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-3-2017-07-20" class="anchor"></a>Version 1.1.3 (2017-07-20)</h2>
-<ul>
-<li>Add verbose option to scDDEstimate</li>
-<li>Change “mean-dropout” to “mean-zeros” in compareSCESets</li>
-</ul>
-</div>
-    <div id="version-1-1-2-2017-07-16" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-2-2017-07-16" class="anchor"></a>Version 1.1.2 (2017-07-16)</h2>
-<ul>
-<li>Update summariseDiff</li>
-<li>Update scDDEstimate, now estimates gene types</li>
-<li>Fix error in lun2Estimate</li>
-<li>Import SummarizedExperiment to avoid warnings</li>
-</ul>
-</div>
-    <div id="version-1-1-1-2017-07-07" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-1-2017-07-07" class="anchor"></a>Version 1.1.1 (2017-07-07)</h2>
-<ul>
-<li>Add batch effects to Splat simulation</li>
-<li>Make Splat group assignment probabilistic</li>
-<li>Update SplatParams with new parameters</li>
-</ul>
-</div>
-    <div id="version-1-1-0-2017-07-07" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-0-2017-07-07" class="anchor"></a>Version 1.1.0 (2017-07-07)</h2>
-<ul>
-<li>Bioconductor 3.6 devel</li>
-</ul>
-</div>
-    <div id="version-1-0-3-2017-05-26" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-0-3-2017-05-26" class="anchor"></a>Version 1.0.3 (2017-05-26)</h2>
-<ul>
-<li>Update citation</li>
-</ul>
-</div>
-    <div id="version-1-0-2-2017-05-15" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-0-2-2017-05-15" class="anchor"></a>Version 1.0.2 (2017-05-15)</h2>
-<ul>
-<li>Fix error handling when fitting means</li>
-</ul>
-</div>
-    <div id="version-1-0-1-2017-04-28" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-0-1-2017-04-28" class="anchor"></a>Version 1.0.1 (2017-04-28)</h2>
-<ul>
-<li>Fix scales in some difference plots</li>
-<li>Fix colours in difference plots</li>
-<li>Fix panel legends</li>
-</ul>
-</div>
-    <div id="version-1-0-0-2017-04-28" class="section level1">
-<h1 class="hasAnchor">
-<a href="#version-1-0-0-2017-04-28" class="anchor"></a>Version 1.0.0 (2017-04-28)</h1>
-<ul>
-<li>Bioconductor 3.5 release</li>
-</ul>
-<div id="version-0-99-15-2017-04-14" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-15-2017-04-14" class="anchor"></a>Version 0.99.15 (2017-04-14)</h2>
-<ul>
-<li>Add summariseDiff function</li>
-<li>Add BPPARAM argument to scDDSimulate</li>
-<li>Adjust default Splat DE factor parameters</li>
-<li>Add limits to zeros diff plots</li>
-<li>Remove estimation of dropout.present</li>
-</ul>
-</div>
-<div id="version-0-99-14-2017-03-28" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-14-2017-03-28" class="anchor"></a>Version 0.99.14 (2017-03-28)</h2>
-<ul>
-<li>Add functions for making comparison panels</li>
-<li>Add panel section to vignette</li>
-<li>Change variance plot scale (for consistency)</li>
-</ul>
-</div>
-<div id="version-0-99-13-2017-03-25" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-13-2017-03-25" class="anchor"></a>Version 0.99.13 (2017-03-25)</h2>
-<ul>
-<li>Modify how Lun2Params stores gene paramters to use data.frame</li>
-<li>Move sampling of genes/cells to lun2Simulate</li>
-<li>Return to old Lun2 nGenes estimate</li>
-</ul>
-</div>
-<div id="version-0-99-12-2017-03-22" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-12-2017-03-22" class="anchor"></a>Version 0.99.12 (2017-03-22)</h2>
-<ul>
-<li>Add diffSCESets function</li>
-<li>Update compareSCESets plots</li>
-<li>Modify Lun2 nGenes estimate</li>
-<li>Modify how addFeatureStats names columns</li>
-<li>Add infinte bcv.df warning to splatSimulate</li>
-</ul>
-</div>
-<div id="version-0-99-11-2017-03-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-11-2017-03-20" class="anchor"></a>Version 0.99.11 (2017-03-20)</h2>
-<ul>
-<li>Add parallel option to lun2Estimate</li>
-<li>Allow non-integer library sizes in Lun2Params</li>
-<li>Adjust dropout eta value</li>
-<li>Adjust comparison plots</li>
-</ul>
-</div>
-<div id="version-0-99-10-2017-03-07" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-10-2017-03-07" class="anchor"></a>Version 0.99.10 (2017-03-07)</h2>
-<ul>
-<li>Improve Splat estimation procedure</li>
-<li>Update default Splat parameters</li>
-<li>Remove out.loProb Splat parameter</li>
-<li>Add MeanZeros plot to compareSCESets</li>
-</ul>
-</div>
-<div id="version-0-99-9-2017-02-02" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-9-2017-02-02" class="anchor"></a>Version 0.99.9 (2017-02-02)</h2>
-<ul>
-<li>Add addGeneLengths function</li>
-<li>Update scDD reference</li>
-</ul>
-</div>
-<div id="version-0-99-8-2017-01-23" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-8-2017-01-23" class="anchor"></a>Version 0.99.8 (2017-01-23)</h2>
-<ul>
-<li>Fix bug that meant non-linear path factors weren’t stored in output</li>
-</ul>
-</div>
-<div id="version-0-99-7-2017-01-10" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-7-2017-01-10" class="anchor"></a>Version 0.99.7 (2017-01-10)</h2>
-<ul>
-<li>Small changes to avoid NOTEs and reduce check time</li>
-</ul>
-</div>
-<div id="version-0-99-6-2016-12-29" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-6-2016-12-29" class="anchor"></a>Version 0.99.6 (2016-12-29)</h2>
-<ul>
-<li>Add installation to vignette</li>
-<li>Add detail about counts matrix to vignette</li>
-<li>Replace 1:x with seq_len/seq_along</li>
-</ul>
-</div>
-<div id="version-0-99-5-2016-12-28" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-5-2016-12-28" class="anchor"></a>Version 0.99.5 (2016-12-28)</h2>
-<ul>
-<li>Set R_TESTS environment</li>
-</ul>
-</div>
-<div id="version-0-99-4-2016-12-23" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-4-2016-12-23" class="anchor"></a>Version 0.99.4 (2016-12-23)</h2>
-<ul>
-<li>Version bump to start build</li>
-</ul>
-</div>
-<div id="version-0-99-3-2016-12-21" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-3-2016-12-21" class="anchor"></a>Version 0.99.3 (2016-12-21)</h2>
-<ul>
-<li>Fix to match Bioconductor version of scDD</li>
-<li>Add logo to repository</li>
-</ul>
-</div>
-<div id="version-0-99-2-2016-12-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-2-2016-12-13" class="anchor"></a>Version 0.99.2 (2016-12-13)</h2>
-<ul>
-<li>Add rownames, colnames to matrices in splatSimulate, lunSimulate</li>
-<li>Bump R version to 3.4</li>
-</ul>
-</div>
-<div id="version-0-99-1-2016-12-12" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-1-2016-12-12" class="anchor"></a>Version 0.99.1 (2016-12-12)</h2>
-<ul>
-<li>Address Biocondutor build warnings, notes</li>
-</ul>
-</div>
-</div>
-    <div id="version-0-99-0-2016-12-05" class="section level1">
-<h1 class="hasAnchor">
-<a href="#version-0-99-0-2016-12-05" class="anchor"></a>Version 0.99.0 (2016-12-05)</h1>
-<ul>
-<li>Submit to Bioconductor</li>
-</ul>
-<div id="version-0-12-1-2016-11-25" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-12-1-2016-11-25" class="anchor"></a>Version 0.12.1 (2016-11-25)</h2>
-<ul>
-<li>Fix bug in compareSCESets</li>
-<li>Dataset order is now kept in plots</li>
-</ul>
-</div>
-<div id="version-0-12-0-2016-10-25" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-12-0-2016-10-25" class="anchor"></a>Version 0.12.0 (2016-10-25)</h2>
-<ul>
-<li>Add compareSCESets function</li>
-<li>Update vignette</li>
-<li>Fix LunParams validity bug</li>
-<li>Add logo</li>
-</ul>
-</div>
-<div id="version-0-11-1-2016-11-23" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-11-1-2016-11-23" class="anchor"></a>Version 0.11.1 (2016-11-23)</h2>
-<ul>
-<li>Fix bug in splatSimulatePaths that caused NAs</li>
-</ul>
-</div>
-<div id="version-0-11-0-2016-11-22" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-11-0-2016-11-22" class="anchor"></a>Version 0.11.0 (2016-11-22)</h2>
-<ul>
-<li>Make compatible with Bioconductor 3.4</li>
-</ul>
-</div>
-<div id="version-0-10-1-2016-10-17" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-10-1-2016-10-17" class="anchor"></a>Version 0.10.1 (2016-10-17)</h2>
-<ul>
-<li>Fix error for SCESets in lun2Estimate, scDDEstimate</li>
-</ul>
-</div>
-<div id="version-0-10-0-2016-10-16" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-10-0-2016-10-16" class="anchor"></a>Version 0.10.0 (2016-10-16)</h2>
-<ul>
-<li>Add listSims function</li>
-<li>Add vignette</li>
-</ul>
-</div>
-<div id="version-0-9-0-2016-10-15" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-9-0-2016-10-15" class="anchor"></a>Version 0.9.0 (2016-10-15)</h2>
-<ul>
-<li>Add scDD simulation</li>
-</ul>
-</div>
-<div id="version-0-8-0-2016-10-15" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-8-0-2016-10-15" class="anchor"></a>Version 0.8.0 (2016-10-15)</h2>
-<ul>
-<li>Add Lun2 simulation</li>
-</ul>
-</div>
-<div id="version-0-7-0-2016-10-14" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-7-0-2016-10-14" class="anchor"></a>Version 0.7.0 (2016-10-14)</h2>
-<ul>
-<li>Redesign how parameters are stored</li>
-<li>Each simulation now has it’s own S4 Params class</li>
-<li>Modify exisiting simulations to use new parameter objects</li>
-</ul>
-</div>
-<div id="version-0-6-0-2016-10-12" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-6-0-2016-10-12" class="anchor"></a>Version 0.6.0 (2016-10-12)</h2>
-<ul>
-<li>Add Lun simulation</li>
-<li>Modify splatParams to take Lun parameters</li>
-</ul>
-</div>
-<div id="version-0-5-0-2016-10-12" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-5-0-2016-10-12" class="anchor"></a>Version 0.5.0 (2016-10-12)</h2>
-<ul>
-<li>Add simple simulation</li>
-</ul>
-</div>
-<div id="version-0-4-0-2016-10-12" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-4-0-2016-10-12" class="anchor"></a>Version 0.4.0 (2016-10-12)</h2>
-<ul>
-<li>Add splatter simulations</li>
-<li>Modify some parts of splatParams and fix bugs</li>
-</ul>
-</div>
-<div id="version-0-3-0-2016-10-06" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-3-0-2016-10-06" class="anchor"></a>Version 0.3.0 (2016-10-06)</h2>
-<ul>
-<li>Added parameter estimation functions</li>
-</ul>
-</div>
-<div id="version-0-2-0-2016-10-06" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-2-0-2016-10-06" class="anchor"></a>Version 0.2.0 (2016-10-06)</h2>
-<ul>
-<li>Added splatParams object</li>
-<li>Added functions for interacting with splatParams</li>
-</ul>
-</div>
-</div>
     </div>
   </div>
 
@@ -457,20 +110,6 @@
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#version-1-1-8-2017-10-13">1.1.8</a></li>
-        <li><a href="#version-1-1-7-2017-10-05">1.1.7</a></li>
-        <li><a href="#version-1-1-6-2017-10-02">1.1.6</a></li>
-        <li><a href="#version-1-1-5-2017-09-13">1.1.5</a></li>
-        <li><a href="#version-1-1-4-2017-08-04">1.1.4</a></li>
-        <li><a href="#version-1-1-3-2017-07-20">1.1.3</a></li>
-        <li><a href="#version-1-1-2-2017-07-16">1.1.2</a></li>
-        <li><a href="#version-1-1-1-2017-07-07">1.1.1</a></li>
-        <li><a href="#version-1-1-0-2017-07-07">1.1.0</a></li>
-        <li><a href="#version-1-0-3-2017-05-26">1.0.3</a></li>
-        <li><a href="#version-1-0-2-2017-05-15">1.0.2</a></li>
-        <li><a href="#version-1-0-1-2017-04-28">1.0.1</a></li>
-        <li><a href="#version-1-0-0-2017-04-28">1.0.0</a></li>
-        <li><a href="#version-0-99-0-2016-12-05">0.99.0</a></li>
       </ul>
     </div>
   </div>
@@ -483,7 +122,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
index ba67f96f9a1acf5b2153caee7614daf0a6514a91..0d69930b40068e9bd51ca8465575c866ca11080b 100644
--- a/docs/reference/BASiCSEstimate.html
+++ b/docs/reference/BASiCSEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -109,10 +109,10 @@
   <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
 
-<span class='co'># S3 method for SCESet</span>
-<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(),
-  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+<span class='co'># S3 method for SingleCellExperiment</span>
+<span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>20000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>burn</span> <span class='kw'>=</span> <span class='fl'>5000</span>,
+  <span class='kw'>params</span> <span class='kw'>=</span> <span class='fu'><a href='newParams.html'>newBASiCSParams</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
 
 <span class='co'># S3 method for matrix</span>
 <span class='fu'>BASiCSEstimate</span>(<span class='no'>counts</span>, <span class='kw'>spike.info</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
@@ -124,8 +124,8 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>counts</th>
-      <td><p>either a counts matrix or an SCESet object containing count
-data to estimate parameters from.</p></td>
+      <td><p>either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.</p></td>
     </tr>
     <tr>
       <th>spike.info</th>
@@ -186,7 +186,10 @@ information is provided there must be at least two batches. See
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
 <span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>spike.info</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(<span class='kw'>Name</span> <span class='kw'>=</span> <span class='fu'>rownames</span>(<span class='no'>sc_example_counts</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>],
                          <span class='kw'>Input</span> <span class='kw'>=</span> <span class='fu'>rnorm</span>(<span class='fl'>10</span>, <span class='fl'>500</span>, <span class='fl'>200</span>),
                          <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
@@ -216,7 +219,7 @@ information is provided there must be at least two batches. See
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/BASiCSParams.html b/docs/reference/BASiCSParams.html
index b15e37bd6414e05eea5cd4ba74d0497c2c1040bc..721e44280c49263924766396eab2f0620eea2a7e 100644
--- a/docs/reference/BASiCSParams.html
+++ b/docs/reference/BASiCSParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -160,7 +160,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
index 4b37c1d6797780df31355f1d692fe9782ed9f3bb..34629d645e635d2f3e2da26bcd401dbf659537f6 100644
--- a/docs/reference/BASiCSSimulate.html
+++ b/docs/reference/BASiCSSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -133,8 +133,8 @@
 
     <p>This function is just a wrapper around <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> that
 takes a <code><a href='BASiCSParams.html'>BASiCSParams</a></code>, runs the simulation then converts the
-output to an <code><a href='http://www.rdocumentation.org/packages/scater/topics/SCESet'>SCESet</a></code> object. See
-<code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> for more details of how the simulation
+output to a <code><a href='http://www.rdocumentation.org/packages/SingleCellExperiment/topics/SingleCellExperiment'>SingleCellExperiment</a></code> object.
+See <code><a href='http://www.rdocumentation.org/packages/BASiCS/topics/BASiCS_Sim'>BASiCS_Sim</a></code> for more details of how the simulation
 works.</p>
     
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
@@ -171,7 +171,7 @@ Single-Cell Sequencing data. PLoS Comput. Biol. (2015).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
index 6d912230a51cc362914aecb3e01db0e38b0fcb58..87d793c939c22681b6237a72cefdaaa31712fb15 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -166,7 +166,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/LunParams.html b/docs/reference/LunParams.html
index 6ec76c4f386ae1fb69eb58a54f9e76065dc05193..c84c8c617c7f9efc18d8c89592758cd4c45e0662 100644
--- a/docs/reference/LunParams.html
+++ b/docs/reference/LunParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -158,7 +158,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/MFAParams.html b/docs/reference/MFAParams.html
index 0038585a753d6c7dbff932a21cf636aadb211748..5e5ac99d70c0080a3e787f3157e5310a4e57fcd8 100644
--- a/docs/reference/MFAParams.html
+++ b/docs/reference/MFAParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ the mfa simulation see <code><a href='mfaSimulate.html'>mfaSimulate</a></code>.<
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/Params.html b/docs/reference/Params.html
index 219c8cd2239ac9e15df1b1ece80087a794775bf8..6825352b634a8fa1825f59ea38b920dad90e6992 100644
--- a/docs/reference/Params.html
+++ b/docs/reference/Params.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -134,7 +134,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PhenoParams.html b/docs/reference/PhenoParams.html
index 79dce00cb9cb926c15759b34cfa0740bcdefcd10..2c75b53dc01849419544edfc830f3f4e3e188076 100644
--- a/docs/reference/PhenoParams.html
+++ b/docs/reference/PhenoParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -144,7 +144,7 @@ see <code><a href='phenoSimulate.html'>phenoSimulate</a></code>.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/SCDDParams.html b/docs/reference/SCDDParams.html
index e819d63d8f52a377b0609803c50ae8d54471b996..c50fe4550f236ba2bbcd3e6ceef3dfd33bb1dd2e 100644
--- a/docs/reference/SCDDParams.html
+++ b/docs/reference/SCDDParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -151,7 +151,7 @@ the scDD simulation see <code><a href='scDDSimulate.html'>scDDSimulate</a></code
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/SimpleParams.html b/docs/reference/SimpleParams.html
index e7512c99c3fae780aa89dd4655e95cd4b3a99119..7149329bd1510066471fc3cbd40c2893e7c8b8d7 100644
--- a/docs/reference/SimpleParams.html
+++ b/docs/reference/SimpleParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -142,7 +142,7 @@ see <code><a href='simpleSimulate.html'>simpleSimulate</a></code>.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/SplatParams.html b/docs/reference/SplatParams.html
index 9a310a42cfa82c34db968d38d81116859d4d956a..160134d922e283fb662ad648da8574b0cba0e346 100644
--- a/docs/reference/SplatParams.html
+++ b/docs/reference/SplatParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -222,7 +222,7 @@ see <code><a href='splatSimulate.html'>splatSimulate</a></code>.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/ZINBParams.html b/docs/reference/ZINBParams.html
index 531f0b99428c90fb54fea5a6c93b55cc50b3cf8b..b20caf51ab9229ff5810d5532db821900241acaa 100644
--- a/docs/reference/ZINBParams.html
+++ b/docs/reference/ZINBParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -141,7 +141,7 @@ see <code><a href='zinbSimulate.html'>zinbSimulate</a></code>.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
index 09f2c7d45453b831d5795b704ef917265ec4d296..84890932c7d71d949e8b51e1371ccddad2912999 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -170,7 +170,7 @@ from those added by analysis packages.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index b6a9822baabea89b856596969d345db80946c8df..55f294bc283f48241998b70eea0611be065f01e5 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -154,14 +154,14 @@ vector.</p>
     <pre class="examples"><div class='input'><span class='co'># Default generate method</span>
 <span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
 <span class='fu'>head</span>(<span class='fu'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#&gt; DataFrame with 6 rows and 3 columns
-#&gt;       Gene     GeneMean    Length
-#&gt;   &lt;factor&gt;    &lt;numeric&gt; &lt;numeric&gt;
-#&gt; 1    Gene1 0.7546303813       885
-#&gt; 2    Gene2 0.1242896647      2280
-#&gt; 3    Gene3 0.1160044662      3160
-#&gt; 4    Gene4 0.1938835897      1612
-#&gt; 5    Gene5 0.0020382615      1890
-#&gt; 6    Gene6 0.0006305612      1488</div><div class='input'># Sample method (human coding genes)
+#&gt;       Gene  GeneMean    Length
+#&gt;   &lt;factor&gt; &lt;numeric&gt; &lt;numeric&gt;
+#&gt; 1    Gene1 0.0370520      3077
+#&gt; 2    Gene2 5.1457391      1099
+#&gt; 3    Gene3 0.2357753       811
+#&gt; 4    Gene4 0.4452486      3692
+#&gt; 5    Gene5 0.1680624      3066
+#&gt; 6    Gene6 0.9869200      1228</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>)
@@ -193,7 +193,7 @@ vector.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/bridge.html b/docs/reference/bridge.html
index 10ca1eb6d96ba4e5021c2f9e007a05b2b48638ab..c92b62b3c3afd42fa89abb6b941eb1b2710eaa8f 100644
--- a/docs/reference/bridge.html
+++ b/docs/reference/bridge.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -156,7 +156,7 @@ a random walk with fixed end points.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/compareSCEs.html b/docs/reference/compareSCEs.html
index d1ec1daae19d927f28f5e2ef4c7ba2a1237eefd7..5d6fb33d7c9a2d60c5aca7caf642ef8025046a3c 100644
--- a/docs/reference/compareSCEs.html
+++ b/docs/reference/compareSCEs.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -170,8 +170,9 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
     
 
     <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'>&lt;-</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'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'>compareSCEs</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='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#&gt; [1] "FeatureData" "PhenoData"   "Plots"      </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#&gt; [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes" "ZerosGene"   
+    <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'>compareSCEs</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>))</div><div class='output co'>#&gt; <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#&gt; <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#&gt; <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#&gt; <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#&gt; [1] "FeatureData" "PhenoData"   "Plots"      </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#&gt; [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes" "ZerosGene"   
 #&gt; [6] "ZerosCell"    "MeanZeros"   </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -195,7 +196,7 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/diffSCEs.html b/docs/reference/diffSCEs.html
index 500f55f6e2ccb6fc2ffb7477b6b443d6092ed1bf..6ee0aef841bcaf1a554fe2cdd8fb988f46571466 100644
--- a/docs/reference/diffSCEs.html
+++ b/docs/reference/diffSCEs.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -192,8 +192,9 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
     
 
     <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'>&lt;-</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'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'>diffSCEs</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='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#&gt; [1] "Reference"   "FeatureData" "PhenoData"   "Plots"       "QQPlots"    </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#&gt; [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes" "ZerosGene"   
+    <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'>diffSCEs</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>)</div><div class='output co'>#&gt; <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#&gt; <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#&gt; <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#&gt; <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#&gt; [1] "Reference"   "FeatureData" "PhenoData"   "Plots"       "QQPlots"    </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#&gt; [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes" "ZerosGene"   
 #&gt; [6] "ZerosCell"    "MeanZeros"   </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -217,7 +218,7 @@ using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplo
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
index 9b7b0e3d2d7fb0c6727155bf415eff3d49b9c435..d6ee6f7e5d5c9e9208e9a900b68f654285d69ff6 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -153,7 +153,7 @@ the number of groups.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/getLNormFactors.html b/docs/reference/getLNormFactors.html
index 522bee79fd9333ac24ed4a0e2db0a46bd4e48c67..c157131adcfb86d85f09ad4d1e936901495cec37 100644
--- a/docs/reference/getLNormFactors.html
+++ b/docs/reference/getLNormFactors.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -156,7 +156,7 @@ from 1.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html
index fce5d8559378bcc3458f9526fc491e45f4e54791..c606e868d166a0ebe075ebb8c5aacd5f176c8439 100644
--- a/docs/reference/getParam.html
+++ b/docs/reference/getParam.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -152,7 +152,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/getParams.html b/docs/reference/getParams.html
index 0090051c4bf79a04d83299d35d1ac3005678cd6a..7a1af5951c39a397004d7e3dd55687a6169dc121 100644
--- a/docs/reference/getParams.html
+++ b/docs/reference/getParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -156,7 +156,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/getPathOrder.html b/docs/reference/getPathOrder.html
index c5be15aaaaa896ce9250145eef24364cdee309b5..87b35c87ccf5e2be63e7efe4129967be7be88326 100644
--- a/docs/reference/getPathOrder.html
+++ b/docs/reference/getPathOrder.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -141,7 +141,7 @@ from.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 5cb5e3398c3b1b55529090eb278472970ab326af..5b7eef7cbb497439fa25b7185d640add3b6bde38 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -100,7 +100,7 @@
     <div class="page-header">
       <h1>
         Reference
-        <small>version&nbsp;1.1.8</small>
+        <small>version&nbsp;1.3.1</small>
       </h1>
     </div>
 
@@ -336,9 +336,9 @@
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="phenoEstimate.html">phenoEstimate</a></code> </p>
+            <p><code><a href="phenoSimulate.html">phenoSimulate</a></code> </p>
           </td>
-          <td><p>Estimate PhenoPath simulation parameters</p></td>
+          <td><p>PhenoPath simulation</p></td>
         </tr><tr>
           <!--  -->
           <td>
@@ -580,7 +580,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index 2393fa095adb1e6eaa7eae4f68698a8810abf187..3c0793ef444a716e681fdf59dab389677b125f61 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -194,7 +194,7 @@ displayed.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html
index 5f8cce0465cda42b03d3d6ed61e9f49d5c924853..c599ed5b8848e61f993a2cfa427c8a589e8a019c 100644
--- a/docs/reference/logistic.html
+++ b/docs/reference/logistic.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -147,7 +147,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
index 981a52b6ac4c56dfcd1225dba9d2fb704891fdb6..2199344bc5362dccd6c786aff88cdf29beb1571d 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -161,8 +161,11 @@ giving the parallel back-end to be used. Default is
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
 <span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
 <span class='fu'>data</span>(<span class='st'>"sc_example_cell_info"</span>)
+
 <span class='no'>plates</span> <span class='kw'>&lt;-</span> <span class='fu'>factor</span>(<span class='no'>sc_example_cell_info</span>$<span class='no'>Mutation_Status</span>)
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>lun2Estimate</span>(<span class='no'>sc_example_counts</span>, <span class='no'>plates</span>, <span class='kw'>min.size</span> <span class='kw'>=</span> <span class='fl'>20</span>)
 <span class='no'>params</span>
@@ -189,7 +192,7 @@ giving the parallel back-end to be used. Default is
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index b4caa06e495f89049b38e68256c146e8484b6120..5efaca28755ef77fd6759e259d465502508b3219 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -185,7 +185,7 @@ expression analyses of single-cell RNA-seq data. Biostatistics (2017).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index d616dc41eca3b506b56ed44d6a7d2c4e0b58bdac..bd18606a92252cfe053fb6b682b16c539218ac4d 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -139,14 +139,17 @@ for more details on the parameters.</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+    <pre class="examples"><div class='input'><span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>lunEstimate</span>(<span class='no'>sc_example_counts</span>)
 <span class='no'>params</span></div><div class='output co'>#&gt; A Params object of class LunParams 
 #&gt; Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. 
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40   736969  
+#&gt;    2000       40   603800  
 #&gt; 
 #&gt; 9 additional parameters 
 #&gt; 
@@ -188,7 +191,7 @@ for more details on the parameters.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
index 31bd82a4d9e1a77d385931ac948c4b4f0b203d45..84ca3dea19be4b33ed29f7e0f7d8c3a79d38462a 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -177,7 +177,7 @@ RNA sequencing data with many zero counts. Genome Biology (2016).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
index 952d7e03ae0fa742e966137455968c5a238f335d..b0184c32a219c0b2a11ab486cd3e0730bc9674a2 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -159,7 +159,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index 91a4c2ecf2af1fea4bfafd7d2375870fc006cfbe..cfabb097a54c05571ccc1ab21f2101d40f3bcbc0 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -159,7 +159,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index 78c41a557bd16aaf909c25a023c2fe4f491356b8..09aab89a32d8366e0aef790cad52c96a45f018b0 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -141,8 +141,8 @@ single panel.</p>
     <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>sim1</span> <span class='kw'>&lt;-</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>)
 <span class='no'>sim2</span> <span class='kw'>&lt;-</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>)
-<span class='no'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'>compSCESets</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='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'>diffSCESets</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'>comparison</span> <span class='kw'>&lt;-</span> <span class='fu'>compSCEs</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='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</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'>panel</span> <span class='kw'>&lt;-</span> <span class='fu'>makeOverallPanel</span>(<span class='no'>comparison</span>, <span class='no'>difference</span>)
 <span class='co'># }</span><div class='input'>
 </div></pre>
@@ -166,7 +166,7 @@ single panel.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index b43414b65a219a848445f1e94afefd0396f2d7f2..ab17ffe31a97db8f87f78c82e4026bed0da3f813 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -140,14 +140,17 @@ details on the parameters.</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+    <pre class="examples"><div class='input'><span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>mfaEstimate</span>(<span class='no'>sc_example_counts</span>)
 <span class='no'>params</span></div><div class='output co'>#&gt; A Params object of class MFAParams 
 #&gt; Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. 
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40   736969  
+#&gt;    2000       40   603800  
 #&gt; 
 #&gt; 4 additional parameters 
 #&gt; 
@@ -185,7 +188,7 @@ details on the parameters.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/mfaSimulate.html b/docs/reference/mfaSimulate.html
index f0365d753ec6394242e02404a28ab09a3f01f52c..2ae55715e72e997799799e0ce24ed991b5635637 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -173,7 +173,7 @@ Open Research (2017).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index 251cb3170c7793aade3520a787c2c3411b4acf52..496c5dab384bd4c1954e9f5f227c7c90d29f1d6e 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -161,7 +161,7 @@ Params subtypes.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 97e7ff6a611b1e15d97df595839dc584064b0029..423f5f1e533e845d8d6292bd1bc95a3da4074dda 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -141,14 +141,17 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+    <pre class="examples"><div class='input'><span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>phenoEstimate</span>(<span class='no'>sc_example_counts</span>)
 <span class='no'>params</span></div><div class='output co'>#&gt; A Params object of class PhenoParams 
 #&gt; Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. 
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40   736969  
+#&gt;    2000       40   603800  
 #&gt; 
 #&gt; 4 additional parameters 
 #&gt; 
@@ -178,7 +181,7 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/phenoSimulate.html b/docs/reference/phenoSimulate.html
index 1d84c2c4e049e029cefe5fc5ec6829f553cf4d12..e6b0404f7a205645e57d94b8c40a265194f0aff7 100644
--- a/docs/reference/phenoSimulate.html
+++ b/docs/reference/phenoSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -176,7 +176,7 @@ and environmental backgrounds across single-cells and populations. bioRxiv
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/rbindMatched.html b/docs/reference/rbindMatched.html
index f7064fb599c626583b0b12a342f1b52fb93b0176..d88500a9c0d2819ad1c3b1274b0af4719331d59c 100644
--- a/docs/reference/rbindMatched.html
+++ b/docs/reference/rbindMatched.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ to both.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index 19ec722e1ad62bedf9456f9952e507c87b8d4f66..19c5dff2c095fbbd71b5471f878ee6df0a3c21b6 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -172,7 +172,10 @@ simulate. The output is then converted to a SCDDParams object. See
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
 <span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>conditions</span> <span class='kw'>&lt;-</span> <span class='fu'>sample</span>(<span class='fl'>1</span>:<span class='fl'>2</span>, <span class='fu'>ncol</span>(<span class='no'>sc_example_counts</span>), <span class='kw'>replace</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>scDDEstimate</span>(<span class='no'>sc_example_counts</span>, <span class='no'>conditions</span>)
 <span class='no'>params</span>
@@ -199,7 +202,7 @@ simulate. The output is then converted to a SCDDParams object. See
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index 397d4b5a9be488614c20e026080bb59adc9dee3c..02caf606417a0e6f2e8a94ecb0289507391cfe24 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -190,7 +190,7 @@ single-cell RNA-seq experiments. Genome Biology (2016).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index d8975e913a431d10446f27806a522837fa53aa8c..0cb1cade4d08d24a2656cae7b1fbd2db491961c2 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -160,7 +160,7 @@
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (Cells)   [Seed]  
-#&gt;     100      100   736969  
+#&gt;     100      100   603800  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
@@ -193,7 +193,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
index c17d16d083f34929258668732830b0be74dabd5f..eb023a41d84931337a7e8da49074f22604b2ae34 100644
--- a/docs/reference/setParamUnchecked.html
+++ b/docs/reference/setParamUnchecked.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -151,7 +151,7 @@ VALIDITY!</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index 72d6c08ee1b49d80cc593c4ebb0fd8cfad2e8a93..0c09452a0f15e26f9433fccd80fd0fbbd64fad8c 100644
--- a/docs/reference/setParams.html
+++ b/docs/reference/setParams.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -146,7 +146,7 @@ them manually), see examples.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (Genes)  (Cells)   [Seed]  
-#&gt;   10000      100   736969  
+#&gt;   10000      100   603800  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
@@ -164,7 +164,7 @@ them manually), see examples.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    1000       50   736969  
+#&gt;    1000       50   603800  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
@@ -182,7 +182,7 @@ them manually), see examples.</p>
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    1000       50   736969  
+#&gt;    1000       50   603800  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
@@ -216,7 +216,7 @@ them manually), see examples.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/setParamsUnchecked.html b/docs/reference/setParamsUnchecked.html
index e88d82d34519ce01667ca4b8ee58acd6e2e06bd0..0d7ea93cf90280470ee7d87457327fe90ff3ba9c 100644
--- a/docs/reference/setParamsUnchecked.html
+++ b/docs/reference/setParamsUnchecked.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -159,7 +159,7 @@ them manually), see examples. THE FINAL OBJECT IS NOT CHECKED FOR VALIDITY!</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/showPP.html b/docs/reference/showPP.html
index 9b91e3b80f5367b3b5a12b1f976db75516ecca99..151a11b2f092942dfb59ab8699f94af165cea4f5 100644
--- a/docs/reference/showPP.html
+++ b/docs/reference/showPP.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -143,7 +143,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
index 43fa74cd6854f6647b848f5d544344cdae30b09f..7fc4405cc618f7a059fab5bb8123b05e0f572a5d 100644
--- a/docs/reference/simpleEstimate.html
+++ b/docs/reference/simpleEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -142,14 +142,17 @@ details on the parameters.</p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+    <pre class="examples"><div class='input'><span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>simpleEstimate</span>(<span class='no'>sc_example_counts</span>)
 <span class='no'>params</span></div><div class='output co'>#&gt; A Params object of class SimpleParams 
 #&gt; Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. 
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40   736969  
+#&gt;    2000       40   603800  
 #&gt; 
 #&gt; 3 additional parameters 
 #&gt; 
@@ -183,7 +186,7 @@ details on the parameters.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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       </footer>
diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
index e96bf35ffcf92fb3721137a2e7c1c313a0e24c6b..cf7047ddfb614ffc48c756324724150a4841c93a 100644
--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -164,7 +164,7 @@ details of the parameters.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatEstBCV.html b/docs/reference/splatEstBCV.html
index 2787af928f78be9c71cc527d3315c6ca057fa042..bc5d7fe51f9b2a1fc038ab16d5de62069fee3871 100644
--- a/docs/reference/splatEstBCV.html
+++ b/docs/reference/splatEstBCV.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -155,7 +155,7 @@ apply a small correction, <code>disp = 0.1 + 0.25 * edgeR.disp</code>.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatEstDropout.html b/docs/reference/splatEstDropout.html
index f00cf74e780a5f48d6edb487159796a46fcaeec0..f275512cc393a29b075fec8e6a16601143466dbf 100644
--- a/docs/reference/splatEstDropout.html
+++ b/docs/reference/splatEstDropout.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -152,7 +152,7 @@ zeros in each gene. See <code><a href='http://www.rdocumentation.org/packages/st
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatEstLib.html b/docs/reference/splatEstLib.html
index c986a2cc9b7d3dea0195b0447cdfc2746f21764a..33e42989f5e1af131871d7ae0035d244a09562d6 100644
--- a/docs/reference/splatEstLib.html
+++ b/docs/reference/splatEstLib.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ parameters are added to the params object. See
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatEstMean.html b/docs/reference/splatEstMean.html
index 4443f94dc1573f4d9baceeddb67a970d98591d1d..91e7ec9bb715aaac9589ade3c12fb1d59c62038e 100644
--- a/docs/reference/splatEstMean.html
+++ b/docs/reference/splatEstMean.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -156,7 +156,7 @@ and 90th percentiles.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
index 647896a9896f4b974bfc3b855a728c02d4a20d79..c9a7b95af1da084aa758e1587843207c9240b061 100644
--- a/docs/reference/splatEstOutlier.html
+++ b/docs/reference/splatEstOutlier.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -157,7 +157,7 @@ scale parameters using <code><a href='http://www.rdocumentation.org/packages/fit
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index 9f05e80243496b1dba1b35239aefe9867acc0e4a..7059e3cfe03a087ff1959f6dab3c2cf4e7265787 100644
--- a/docs/reference/splatEstimate.html
+++ b/docs/reference/splatEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -142,14 +142,17 @@ containing count data to estimate parameters from.</p></td>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+    <pre class="examples"><div class='input'><span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
+<span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>splatEstimate</span>(<span class='no'>sc_example_counts</span>)
 <span class='no'>params</span></div><div class='output co'>#&gt; A Params object of class SplatParams 
 #&gt; Parameters can be (estimable) or [not estimable], 'Default' or 'NOT DEFAULT'. 
 #&gt; 
 #&gt; Global: 
 #&gt; (GENES)  (CELLS)   [Seed]  
-#&gt;    2000       40   736969  
+#&gt;    2000       40   603800  
 #&gt; 
 #&gt; 27 additional parameters 
 #&gt; 
@@ -211,7 +214,7 @@ containing count data to estimate parameters from.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
index 7e0c42284bda2151802ffbaf65c12907050e6088..5d210d3a8f914b96c50c7f46d07f81c2688de284 100644
--- a/docs/reference/splatSimBCVMeans.html
+++ b/docs/reference/splatSimBCVMeans.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ and inverse gamma distribution.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
index 5600e9430a9763870a8e484db31f1828f4e99360..66a3a1ed4d51078240c62c43138d8e5136b522c4 100644
--- a/docs/reference/splatSimBatchCellMeans.html
+++ b/docs/reference/splatSimBatchCellMeans.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -144,7 +144,7 @@ factors.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index 1b059e35b8c711fffb44d4d684d12683336b118b..920063de9fc083caf2deb18afcc5c35cba2ae59e 100644
--- a/docs/reference/splatSimBatchEffects.html
+++ b/docs/reference/splatSimBatchEffects.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ means for each batch.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index cb90535a07415a3082bcb67920746df4b51a36fb..522d75dc9bc16659328c3345c45f3e98ec84eac6 100644
--- a/docs/reference/splatSimCellMeans.html
+++ b/docs/reference/splatSimCellMeans.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -151,7 +151,7 @@ means are adjusted for each cell's expected library size.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
index cf9c9e94befc0a78e6c3baf2a105a1abb182e9d1..a84b65c1e3a7a9b7e7480fe9a3aa299686ebf356 100644
--- a/docs/reference/splatSimDE.html
+++ b/docs/reference/splatSimDE.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -148,7 +148,7 @@ they are simulated in the correct order.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
index bcff9a23311d82a515e78c857e8308e2a4f1e8e1..1387020f260fef1dd3d421b2f2ee86c107d5f3a2 100644
--- a/docs/reference/splatSimDropout.html
+++ b/docs/reference/splatSimDropout.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -146,7 +146,7 @@ to decide which counts should be dropped.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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       </footer>
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index 4ac63ab88bb97720a9b86ae8b1c5725ede40217d..f55e7e40a4d11fa8f06b2e6d6b17a39afcb5b1d4 100644
--- a/docs/reference/splatSimGeneMeans.html
+++ b/docs/reference/splatSimGeneMeans.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ with the median mean expression multiplied by the outlier factor.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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       </footer>
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index a8cb353d521c96b48d71dfd4e0d8be4a5047de98..69ee1cbaa6f334823573b6e3b82341bbb7ea6f89 100644
--- a/docs/reference/splatSimLibSizes.html
+++ b/docs/reference/splatSimLibSizes.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -143,7 +143,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index 6f0ed0f8f1ede60ff8a6ec4189dbabc5ad652cd4..55f89b76eede5c6d4931265a87f1bd2e81c8d7f3 100644
--- a/docs/reference/splatSimTrueCounts.html
+++ b/docs/reference/splatSimTrueCounts.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -145,7 +145,7 @@ group (or path position), expected library size and BCV.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index 28ffcac03953ae094e8a8a1dbfba4e7a4cb1f17a..5ec04af36a1b29182a1ce6d3019cd55cd908fed5 100644
--- a/docs/reference/splatSimulate.html
+++ b/docs/reference/splatSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -268,7 +268,7 @@ sequencing data. Genome Biology (2017).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
index 3bcc5e2822d2234bdd88cae7abd1a5d43bdcb666..63791c0c53f1d21624a1e666b345b47c5d500b54 100644
--- a/docs/reference/splatter.html
+++ b/docs/reference/splatter.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -137,7 +137,7 @@ Sequencing Data. bioRxiv. 2017; doi:10.1101/133173</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 552d74d58c8cf57bff21794fc268d57f54183678..c0fb1a0deaa0c0246d35c093a66d3e93b711b5c8 100644
--- a/docs/reference/summariseDiff.html
+++ b/docs/reference/summariseDiff.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
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-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -124,22 +124,23 @@ 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'>&lt;-</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'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</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'>&lt;-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
+    <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Getting parameters...</span></div><div class='output co'>#&gt; <span class='message'>Creating simulation object...</span></div><div class='output co'>#&gt; <span class='message'>Simulating library sizes...</span></div><div class='output co'>#&gt; <span class='message'>Simulating gene means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating BCV...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts..</span></div><div class='output co'>#&gt; <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#&gt; <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'>&lt;-</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'>#&gt; <span class='message'>Simulating means...</span></div><div class='output co'>#&gt; <span class='message'>Simulating counts...</span></div><div class='output co'>#&gt; <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</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>)</div><div class='output co'>#&gt; <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#&gt; <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#&gt; <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#&gt; <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='no'>summary</span> <span class='kw'>&lt;-</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'>#&gt;   Dataset Statistic          MAD MADScaled MADRank          MAE MAEScaled
-#&gt; 1   Splat      Mean     2.757589       NaN       1     2.651957       NaN
-#&gt; 2   Splat  Variance    10.467288       NaN       1    10.272985       NaN
-#&gt; 3   Splat ZerosGene    40.000000       NaN       1    44.935000       NaN
-#&gt; 4   Splat   MeanVar     9.682925       NaN       1    12.193247       NaN
-#&gt; 5   Splat MeanZeros    45.000000       NaN       1    44.460000       NaN
-#&gt; 6   Splat   LibSize 56511.000000       NaN       1 59458.300000       NaN
+#&gt; 1   Splat      Mean 3.545552e+00       NaN       1 3.129809e+00       NaN
+#&gt; 2   Splat  Variance 7.591704e-02       NaN       1 1.200872e-01       NaN
+#&gt; 3   Splat ZerosGene 3.500000e+01       NaN       1 4.185500e+01       NaN
+#&gt; 4   Splat   MeanVar 4.092154e-01       NaN       1 4.692433e-01       NaN
+#&gt; 5   Splat MeanZeros 4.500000e+01       NaN       1 4.415500e+01       NaN
+#&gt; 6   Splat   LibSize 6.258000e+04       NaN       1 6.246590e+04       NaN
 #&gt;   MAERank         RMSE RMSEScaled RMSERank
-#&gt; 1       1     3.182101        NaN        1
-#&gt; 2       1    13.133714        NaN        1
-#&gt; 3       1    48.428039        NaN        1
-#&gt; 4       1    15.352203        NaN        1
-#&gt; 5       1    53.898052        NaN        1
-#&gt; 6       1 61094.139540        NaN        1</div></pre>
+#&gt; 1       1 3.498988e+00        NaN        1
+#&gt; 2       1 1.702264e-01        NaN        1
+#&gt; 3       1 4.627229e+01        NaN        1
+#&gt; 4       1 5.756617e-01        NaN        1
+#&gt; 5       1 5.414541e+01        NaN        1
+#&gt; 6       1 6.399102e+04        NaN        1</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -160,7 +161,7 @@ Error (RMSE) for the various properties and ranks them.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
index 320f7ea7925795103fadf35f30a2d31adfc803e8..f5a1067dbf341aa2441f19d44b396f44ed2a5752 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -143,7 +143,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
index 5bd42b014258b50ed8063b89c99d272c9e76ca1f..f838ec1e21aa8a08650f43ffa05cab8052d029cd 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -189,7 +189,10 @@ the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParam
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='co'># Load example data</span>
+<span class='fu'>library</span>(<span class='no'>scater</span>)
 <span class='fu'>data</span>(<span class='st'>"sc_example_counts"</span>)
+
 <span class='no'>params</span> <span class='kw'>&lt;-</span> <span class='fu'>zinbEstimate</span>(<span class='no'>sc_example_counts</span>)
 <span class='no'>params</span>
 <span class='co'># }</span></pre>
@@ -215,7 +218,7 @@ the fitted model and inserts it into a <code><a href='ZINBParams.html'>ZINBParam
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/zinbSimulate.html b/docs/reference/zinbSimulate.html
index 2dea5b285307787c5c4a91773dfe5dbc2375b805..bfd11132c438b8bf747cead2c4ab3e9c23c04300 100644
--- a/docs/reference/zinbSimulate.html
+++ b/docs/reference/zinbSimulate.html
@@ -64,7 +64,7 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="..//index.html">
+  <a href="../index.html">
     <span class="fa fa-home fa-lg"></span>
      
   </a>
@@ -176,7 +176,7 @@ bioRxiv (2017).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/index.md b/index.md
index 24e894f7a1b4da355ce2c483c692121cf395e223..90cfdc6369d87c00d275d3d441b1f04cbca521f9 100644
--- a/index.md
+++ b/index.md
@@ -16,8 +16,8 @@ data. Splatter provides a common interface to multiple simulations that have:
 * 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.
+[`SingleCellExperiment`][SCE] 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
@@ -45,7 +45,7 @@ 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 
+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.
 
@@ -73,6 +73,7 @@ devtools::install("Oshlack/splatter")
 ```
 
 [scater]: https://github.com/davismcc/scater
+[SCE]: https://github.com/drisso/SingleCellExperiment
 [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/
diff --git a/man/BASiCSEstimate.Rd b/man/BASiCSEstimate.Rd
index 0fabfebad0e5f63082e073c8eb9913d0bb97bae3..aa9c6a3109041c691695b1b079ad914c7953c2d3 100644
--- a/man/BASiCSEstimate.Rd
+++ b/man/BASiCSEstimate.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/BASiCS-estimate.R
 \name{BASiCSEstimate}
 \alias{BASiCSEstimate}
-\alias{BASiCSEstimate.SCESet}
+\alias{BASiCSEstimate.SingleCellExperiment}
 \alias{BASiCSEstimate.matrix}
 \title{Estimate BASiCS simulation parameters}
 \usage{
@@ -10,17 +10,17 @@ BASiCSEstimate(counts, spike.info = NULL, batch = NULL, n = 20000,
   thin = 10, burn = 5000, params = newBASiCSParams(), verbose = TRUE,
   progress = TRUE, ...)
 
-\method{BASiCSEstimate}{SCESet}(counts, spike.info = NULL, batch = NULL,
-  n = 20000, thin = 10, burn = 5000, params = newBASiCSParams(),
-  verbose = TRUE, progress = TRUE, ...)
+\method{BASiCSEstimate}{SingleCellExperiment}(counts, spike.info = NULL,
+  batch = NULL, n = 20000, thin = 10, burn = 5000,
+  params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...)
 
 \method{BASiCSEstimate}{matrix}(counts, spike.info = NULL, batch = NULL,
   n = 20000, thin = 10, burn = 5000, params = newBASiCSParams(),
   verbose = TRUE, progress = TRUE, ...)
 }
 \arguments{
-\item{counts}{either a counts matrix or an SCESet object containing count
-data to estimate parameters from.}
+\item{counts}{either a counts matrix or a SingleCellExperiment object
+containing count data to estimate parameters from.}
 
 \item{spike.info}{data.frame describing spike-ins with two columns: "Name"
 giving the names of the spike-in features (must match
@@ -61,7 +61,10 @@ information is provided there must be at least two batches. See
 }
 \examples{
 \dontrun{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10],
                          Input = rnorm(10, 500, 200),
                          stringsAsFactors = FALSE)
diff --git a/man/BASiCSSimulate.Rd b/man/BASiCSSimulate.Rd
index cc92db054bd1f6f8259a9315258eb7719c4736cd..9a26e0d14e88a7cd42945651af0a26f882999ea4 100644
--- a/man/BASiCSSimulate.Rd
+++ b/man/BASiCSSimulate.Rd
@@ -23,8 +23,8 @@ Simulate counts using the BASiCS method.
 \details{
 This function is just a wrapper around \code{\link[BASiCS]{BASiCS_Sim}} that
 takes a \code{\link{BASiCSParams}}, runs the simulation then converts the
-output to an \code{\link[scater]{SCESet}} object. See
-\code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
+output to a \code{\link[SingleCellExperiment]{SingleCellExperiment}} object.
+See \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
 works.
 }
 \examples{
diff --git a/man/lun2Estimate.Rd b/man/lun2Estimate.Rd
index d0e240edbbdc6d983727a0e63d4f98e68ccb9283..b4b1af2023b33b499f29830f89d011bb3f144cca 100644
--- a/man/lun2Estimate.Rd
+++ b/man/lun2Estimate.Rd
@@ -44,8 +44,11 @@ See \code{\link{Lun2Params}} for more details on the parameters.
 }
 \examples{
 \dontrun{
+# Load example data
+library(scater)
 data("sc_example_counts")
 data("sc_example_cell_info")
+
 plates <- factor(sc_example_cell_info$Mutation_Status)
 params <- lun2Estimate(sc_example_counts, plates, min.size = 20)
 params
diff --git a/man/lunEstimate.Rd b/man/lunEstimate.Rd
index 82f5e670b199dc49e618014924c6273be5cc5f12..63bd4f66b0acd9470701fa4e230c27e1cbcbf98c 100644
--- a/man/lunEstimate.Rd
+++ b/man/lunEstimate.Rd
@@ -30,7 +30,10 @@ input data. No other parameters are estimated. See \code{\link{LunParams}}
 for more details on the parameters.
 }
 \examples{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 params <- lunEstimate(sc_example_counts)
 params
 }
diff --git a/man/makeOverallPanel.Rd b/man/makeOverallPanel.Rd
index 51b219ba7ce6a8d3a77502085bc2c793b313c4b9..e6d54243855bdd2dad54b57f6cbbe8e6c9e18fbc 100644
--- a/man/makeOverallPanel.Rd
+++ b/man/makeOverallPanel.Rd
@@ -29,8 +29,8 @@ single panel.
 \dontrun{
 sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
-comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
-difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+comparison <- compSCEs(list(Splat = sim1, Simple = sim2))
+difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
 panel <- makeOverallPanel(comparison, difference)
 }
 
diff --git a/man/mfaEstimate.Rd b/man/mfaEstimate.Rd
index 002cd047b58ec935bdd1f421756597d8cedb6549..ac81d6a541893ffd4d6d7c4f1de585e6dc8300ab 100644
--- a/man/mfaEstimate.Rd
+++ b/man/mfaEstimate.Rd
@@ -31,7 +31,10 @@ input data. The dropout lambda parameter is estimate using
 details on the parameters.
 }
 \examples{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 params <- mfaEstimate(sc_example_counts)
 params
 }
diff --git a/man/phenoEstimate.Rd b/man/phenoEstimate.Rd
index 5b698238acbc48c4a606cc9fd7a2c3b550936311..1c102ba3d2f02c73a5d5101298d5bfa7cac957ed 100644
--- a/man/phenoEstimate.Rd
+++ b/man/phenoEstimate.Rd
@@ -32,7 +32,10 @@ input data. The total number of genes is evenly divided into the four types.
 See \code{\link{PhenoParams}} for more details on the parameters.
 }
 \examples{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 params <- phenoEstimate(sc_example_counts)
 params
 }
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index 265183465ffcd3ca73550931c721146c38f57611..3b7d9ca9e92c199aadd27d218578d6dafb9e86ed 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -53,7 +53,10 @@ simulate. The output is then converted to a SCDDParams object. See
 }
 \examples{
 \dontrun{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
 params <- scDDEstimate(sc_example_counts, conditions)
 params
diff --git a/man/simpleEstimate.Rd b/man/simpleEstimate.Rd
index 159c87953cde355894abcd344b60ee8ce5106fd3..441accff81ae11b622594476e13ff0ce206a9531 100644
--- a/man/simpleEstimate.Rd
+++ b/man/simpleEstimate.Rd
@@ -33,7 +33,10 @@ to the library size normalised mean expression level using
 details on the parameters.
 }
 \examples{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 params <- simpleEstimate(sc_example_counts)
 params
 }
diff --git a/man/splatEstimate.Rd b/man/splatEstimate.Rd
index b14d5195af99f9d04700f1bd300487cdfc8c951b..736f41b02d235c96b7097350ffc71e55cd0fc879 100644
--- a/man/splatEstimate.Rd
+++ b/man/splatEstimate.Rd
@@ -28,7 +28,10 @@ dataset. See the individual estimation functions for more details on how this
 is done.
 }
 \examples{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 params <- splatEstimate(sc_example_counts)
 params
 }
diff --git a/man/zinbEstimate.Rd b/man/zinbEstimate.Rd
index 7d819e37f7a930b0ee15d1991db1dc406c6396ae..13c7cc1e341b24774077b719c7fe59215412b9e0 100644
--- a/man/zinbEstimate.Rd
+++ b/man/zinbEstimate.Rd
@@ -62,7 +62,10 @@ the fitted model and inserts it into a \code{\link{ZINBParams}} object. See
 }
 \examples{
 \dontrun{
+# Load example data
+library(scater)
 data("sc_example_counts")
+
 params <- zinbEstimate(sc_example_counts)
 params
 }
diff --git a/tests/testthat/test-BASiCSParams.R b/tests/testthat/test-BASiCSParams.R
index 541abc15815caaa54b6f0ec4b5fff2c35e158e7b..97866e7e63fe6bbae2d8994faf9764526f806687 100644
--- a/tests/testthat/test-BASiCSParams.R
+++ b/tests/testthat/test-BASiCSParams.R
@@ -1,7 +1,12 @@
 context("BASiCSParams")
 
+params <- newBASiCSParams()
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class BASiCSParams")
+})
+
 test_that("gene.params checks work", {
-    params <- newBASiCSParams()
     expect_error(setParam(params, "gene.params", data.frame(A = 1, B = 1)),
                  "gene.params: Incorrect column names")
     expect_error(setParam(params, "gene.params",
@@ -10,7 +15,6 @@ test_that("gene.params checks work", {
 })
 
 test_that("cell.params checks work", {
-    params <- newBASiCSParams()
     expect_error(setParam(params, "cell.params", data.frame(A = 1, B = 1)),
                  "cell.params: Incorrect column names")
     expect_error(setParam(params, "cell.params",
@@ -19,9 +23,14 @@ test_that("cell.params checks work", {
 })
 
 test_that("nBatches checks work", {
-    params <- newBASiCSParams()
     expect_error(setParam(params, "nCells", 1),
                  "nCells cannot be set directly, set batchCells instead")
     expect_error(setParam(params, "nBatches", 1),
                  "nBatches cannot be set directly, set batchCells instead")
 })
+
+test_that("batchCells checks work", {
+    pp <- setParam(params, "batchCells", c(10, 10))
+    expect_equal(getParam(pp, "nCells"), 20)
+    expect_equal(getParam(pp, "nBatches"), 2)
+})
diff --git a/tests/testthat/test-Lun2Params.R b/tests/testthat/test-Lun2Params.R
index 5fb60621ad864a0f04ae7f1b2297f7a2b37dc167..98d424f8f540f4a64a32dfadfe3925da0bc43111 100644
--- a/tests/testthat/test-Lun2Params.R
+++ b/tests/testthat/test-Lun2Params.R
@@ -1,7 +1,12 @@
 context("Lun2Params")
 
+params <- newLun2Params()
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class Lun2Params")
+})
+
 test_that("nCells checks work", {
-    params <- newLun2Params()
     expect_error(setParam(params, "nCells", 1),
                  "nCells cannot be set directly, set cell.plates instead")
     expect_error(setParam(params, "nPlates", 1),
@@ -9,7 +14,6 @@ test_that("nCells checks work", {
 })
 
 test_that("gene.params checks work", {
-    params <- newLun2Params()
     expect_error(setParam(params, "gene.params", data.frame(A = 1, B = 1)),
                  "gene.params: Incorrect column names")
     expect_error(setParam(params, "gene.params",
diff --git a/tests/testthat/test-LunParams.R b/tests/testthat/test-LunParams.R
new file mode 100644
index 0000000000000000000000000000000000000000..5f5720bdc56cd62d78403410424748ea4b2b16ac
--- /dev/null
+++ b/tests/testthat/test-LunParams.R
@@ -0,0 +1,17 @@
+context("LunParams")
+
+params <- newLunParams()
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class LunParams")
+})
+
+test_that("nCells checks work", {
+    expect_error(setParam(params, "nCells", 1),
+                 "nCells cannot be set directly, set groupCells instead")
+})
+
+test_that("nGroups checks work", {
+    expect_error(setParam(params, "nGroups", 1),
+                 "nGroups cannot be set directly, set groupCells instead")
+})
diff --git a/tests/testthat/test-MFAEstimate.R b/tests/testthat/test-MFAEstimate.R
new file mode 100644
index 0000000000000000000000000000000000000000..12cee5cc796b64d179c173e2f1b5583f2fb52edb
--- /dev/null
+++ b/tests/testthat/test-MFAEstimate.R
@@ -0,0 +1,9 @@
+context("MFAEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("MFAEstimate works", {
+    params <- mfaEstimate(sc_example_counts)
+    expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-MFAParams.R b/tests/testthat/test-MFAParams.R
new file mode 100644
index 0000000000000000000000000000000000000000..1cd9c19990ff0e3bf06c2c30532f23d828662738
--- /dev/null
+++ b/tests/testthat/test-MFAParams.R
@@ -0,0 +1,7 @@
+context("MFAParams")
+
+params <- newMFAParams()
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class MFAParams")
+})
diff --git a/tests/testthat/test-PhenoParams.R b/tests/testthat/test-PhenoParams.R
index d5a252daba9f5f300840bc949f8a199b79d6e7a1..d806e99a73ea7b757954fdc0b56989e5ced38297 100644
--- a/tests/testthat/test-PhenoParams.R
+++ b/tests/testthat/test-PhenoParams.R
@@ -1,15 +1,20 @@
 context("PhenoParams")
 
+params <- newPhenoParams()
+
 test_that("constructor is valid", {
-    expect_true(validObject(newPhenoParams()))
+    expect_true(validObject(params))
+})
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class PhenoParams")
 })
 
 test_that("nGenes checks work", {
-    params <- newPhenoParams()
     expect_error(setParam(params, "nGenes", 1),
                  "nGenes cannot be set directly")
-    params <- setParam(params, "n.de", 0)
-    total <- getParam(params, "n.de") + getParam(params, "n.pst") +
-             getParam(params, "n.pst.beta") + getParam(params, "n.de.pst.beta")
-    expect_equal(getParam(params, "nGenes"), total)
+    pp <- setParam(params, "n.de", 0)
+    total <- getParam(pp, "n.de") + getParam(pp, "n.pst") +
+             getParam(pp, "n.pst.beta") + getParam(pp, "n.de.pst.beta")
+    expect_equal(getParam(pp, "nGenes"), total)
 })
diff --git a/tests/testthat/test-SCDDParams.R b/tests/testthat/test-SCDDParams.R
index da4d061f8021462f833694061cdee509d35e4558..05ff5ef034d478516785e809e9d4edae650fca9d 100644
--- a/tests/testthat/test-SCDDParams.R
+++ b/tests/testthat/test-SCDDParams.R
@@ -1,17 +1,22 @@
 context("SCDDParams")
 
+params <- newSCDDParams()
+
 test_that("constructor is valid", {
-    expect_true(validObject(newSCDDParams()))
+    expect_true(validObject(params))
+})
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class SCDDParams")
 })
 
 test_that("nGenes checks work", {
-    params <- newSCDDParams()
     expect_error(setParam(params, "nGenes", 1),
                  paste("nGenes cannot be set directly, set nDE, nDP, nDM, nDB,",
                        "nEE or nEP instead"))
-    params <- setParam(params, "nEE", 0)
-    total <- getParam(params, "nDE") + getParam(params, "nDP") +
-             getParam(params, "nDM") + getParam(params, "nDP") +
-             getParam(params, "nEE") + getParam(params, "nEP")
-    expect_equal(getParam(params, "nGenes"), total)
-})
\ No newline at end of file
+    pp <- setParam(params, "nEE", 0)
+    total <- getParam(pp, "nDE") + getParam(pp, "nDP") +
+             getParam(pp, "nDM") + getParam(pp, "nDP") +
+             getParam(pp, "nEE") + getParam(pp, "nEP")
+    expect_equal(getParam(pp, "nGenes"), total)
+})
diff --git a/tests/testthat/test-SCE-functions.R b/tests/testthat/test-SCE-functions.R
new file mode 100644
index 0000000000000000000000000000000000000000..973cf545010fdb66ea3e9f80959e1115abde5a20
--- /dev/null
+++ b/tests/testthat/test-SCE-functions.R
@@ -0,0 +1,37 @@
+context("SCE functions")
+
+sce <- simpleSimulate()
+
+test_that("addFeatureStats works with counts", {
+    ss <- addFeatureStats(sce)
+    expect_true(all(c("MeanCounts", "VarCounts", "CVCounts", "MedCounts",
+                      "MADCounts") %in% colnames(rowData(ss))))
+    ss <- addFeatureStats(sce, log = TRUE)
+    expect_true(all(c("MeanLogCounts", "VarLogCounts", "CVLogCounts",
+                      "MedLogCounts", "MADLogCounts") %in%
+                    colnames(rowData(ss))))
+    ss <- addFeatureStats(sce, no.zeros = TRUE)
+    expect_true(all(c("MeanCountsNo0", "VarCountsNo0", "CVCountsNo0",
+                      "MedCountsNo0", "MADCountsNo0") %in%
+                        colnames(rowData(ss))))
+    ss <- addFeatureStats(sce, log = TRUE, no.zeros = TRUE)
+    expect_true(all(c("MeanLogCountsNo0", "VarLogCountsNo0", "CVLogCountsNo0",
+                      "MedLogCountsNo0", "MADLogCountsNo0") %in%
+                        colnames(rowData(ss))))
+})
+
+test_that("addGeneLengths generate method works", {
+    expect_silent(addGeneLengths(sce))
+    expect_error(addGeneLengths("a"))
+    expect_error(addGeneLengths(sce, loc = "a"))
+    expect_error(addGeneLengths(sce, scale = "a"))
+    expect_error(addGeneLengths(sce, scale = -1))
+})
+
+test_that("addGeneLength sample method works", {
+    lens <- round(runif(100, 100, 10000))
+    expect_silent(addGeneLengths(sce, method = "sample", lengths = lens))
+    expect_error(addGeneLengths(sce, method = "sample"))
+    expect_error(addGeneLengths(sce, method = "sample"), lengths = 0)
+    expect_error(addGeneLengths(sce, method = "sample"), lengths = "a")
+})
diff --git a/tests/testthat/test-SCESet-functions.R b/tests/testthat/test-SCESet-functions.R
deleted file mode 100644
index cfbac01472fc1397bc3b5a2d47ecce65b30e0c29..0000000000000000000000000000000000000000
--- a/tests/testthat/test-SCESet-functions.R
+++ /dev/null
@@ -1,19 +0,0 @@
-context("SCESet functions")
-
-test_that("addGeneLengths generate method works", {
-    sce <- simpleSimulate()
-    expect_silent(addGeneLengths(sce))
-    expect_error(addGeneLengths("a"))
-    expect_error(addGeneLengths(sce, loc = "a"))
-    expect_error(addGeneLengths(sce, scale = "a"))
-    expect_error(addGeneLengths(sce, scale = -1))
-})
-
-test_that("addGeneLength sample method works", {
-    sce <- simpleSimulate()
-    lens <- round(runif(100, 100, 10000))
-    expect_silent(addGeneLengths(sce, method = "sample", lengths = lens))
-    expect_error(addGeneLengths(sce, method = "sample"))
-    expect_error(addGeneLengths(sce, method = "sample"), lengths = 0)
-    expect_error(addGeneLengths(sce, method = "sample"), lengths = "a")
-})
diff --git a/tests/testthat/test-SimpleParams.R b/tests/testthat/test-SimpleParams.R
new file mode 100644
index 0000000000000000000000000000000000000000..3fa78dc650bded2279c5f6298882737dafff4a9c
--- /dev/null
+++ b/tests/testthat/test-SimpleParams.R
@@ -0,0 +1,7 @@
+context("SimpleParams")
+
+params <- newSimpleParams()
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class SimpleParams")
+})
diff --git a/tests/testthat/test-SplatParams.R b/tests/testthat/test-SplatParams.R
index 208f0dfa24b672635f12709d4823b49cdaa3c7d7..91695dfdb193fb493c224e30b8e19f8a1a908d88 100644
--- a/tests/testthat/test-SplatParams.R
+++ b/tests/testthat/test-SplatParams.R
@@ -1,7 +1,12 @@
 context("SplatParams")
 
+params <- newSplatParams()
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class SplatParams")
+})
+
 test_that("nBatches checks work", {
-  params <- newSplatParams()
   expect_error(setParam(params, "nCells", 1),
                "nCells cannot be set directly, set batchCells instead")
   expect_error(setParam(params, "nBatches", 1),
@@ -9,22 +14,20 @@ test_that("nBatches checks work", {
 })
 
 test_that("nGroups checks work", {
-    params <- newSplatParams()
     expect_error(setParam(params, "nGroups", 1),
                  "nGroups cannot be set directly, set group.prob instead")
 })
 
 test_that("path.from checks work", {
-    params <- newSplatParams()
-    params <- setParams(params, group.prob = c(0.5, 0.5))
-    params <- setParamUnchecked(params, "path.from", c(0, 1))
-    expect_silent(validObject(params))
-    params <- setParamUnchecked(params, "path.from", c(0, 3))
-    expect_error(validObject(params), "invalid class")
-    params <- setParamUnchecked(params, "path.from", c(1, 0))
-    expect_error(validObject(params), "path cannot begin at itself")
-    params <- newSplatParams()
-    params <- setParams(params, group.prob = c(0.3, 0.3, 0.4))
-    params <- setParamUnchecked(params, "path.from", c(2, 1, 1))
-    expect_error(validObject(params), "origin must be specified in path.from")
+    pp <- setParams(params, group.prob = c(0.5, 0.5))
+    pp <- setParamUnchecked(pp, "path.from", c(0, 1))
+    expect_silent(validObject(pp))
+    pp <- setParamUnchecked(pp, "path.from", c(0, 3))
+    expect_error(validObject(pp), "invalid class")
+    pp <- setParamUnchecked(pp, "path.from", c(1, 0))
+    expect_error(validObject(pp), "path cannot begin at itself")
+    pp <- newSplatParams()
+    pp <- setParams(pp, group.prob = c(0.3, 0.3, 0.4))
+    pp <- setParamUnchecked(pp, "path.from", c(2, 1, 1))
+    expect_error(validObject(pp), "origin must be specified in path.from")
 })
diff --git a/tests/testthat/test-ZINBParams.R b/tests/testthat/test-ZINBParams.R
index bbb7abd371aa1cddae7f7332201fe10bfc209f62..061bb8ae7675db988e532f112cdf24cf4dea822a 100644
--- a/tests/testthat/test-ZINBParams.R
+++ b/tests/testthat/test-ZINBParams.R
@@ -1,11 +1,16 @@
 context("ZINBParams")
 
+params <- newZINBParams()
+
 test_that("constructor is valid", {
-    expect_true(validObject(newZINBParams()))
+    expect_true(validObject(params))
+})
+
+test_that("printing works", {
+    expect_output(show(params), "A Params object of class ZINBParams")
 })
 
 test_that("nGenes checks work", {
-    params <- newZINBParams()
     expect_error(setParam(params, "nGenes", 1),
                  "nGenes cannot be set directly")
     expect_error(setParam(params, "nCells", 1),
diff --git a/tests/testthat/test-compare.R b/tests/testthat/test-compare.R
new file mode 100644
index 0000000000000000000000000000000000000000..04d652082f78507a9edfa5fa0da889c5f4d4e59b
--- /dev/null
+++ b/tests/testthat/test-compare.R
@@ -0,0 +1,59 @@
+context("Comparison functions")
+
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
+sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
+
+comparison <- compareSCEs(list(Splat = sim1, Simple = sim2))
+difference <- diffSCEs(list(Splat = sim1, Simple = sim2), ref = "Simple")
+
+test_that("compareSCEs works", {
+    expect_length(comparison, 3)
+    expect_true(all(c("FeatureData", "PhenoData", "Plots") %in%
+                        names(comparison)))
+    checkmate::expect_class(comparison$PhenoData, "data.frame")
+    checkmate::expect_class(comparison$FeatureData, "data.frame")
+    expect_length(comparison$Plots, 7)
+    expect_true(all(c("Means", "Variances", "MeanVar", "LibrarySizes",
+                      "ZerosGene", "ZerosCell", "MeanZeros") %in%
+                        names(comparison$Plots)))
+    for (plot in names(comparison$Plots)) {
+        checkmate::expect_class(comparison$Plots[[plot]], "ggplot")
+    }
+})
+
+test_that("diffSCEs works", {
+    expect_length(difference, 5)
+    expect_true(all(c("Reference", "FeatureData", "PhenoData", "Plots",
+                      "QQPlots") %in% names(difference)))
+    checkmate::expect_class(difference$Reference, "SingleCellExperiment")
+    checkmate::expect_class(difference$PhenoData, "data.frame")
+    checkmate::expect_class(difference$FeatureData, "data.frame")
+    expect_length(difference$Plots, 7)
+    expect_true(all(c("Means", "Variances", "MeanVar", "LibrarySizes",
+                      "ZerosGene", "ZerosCell", "MeanZeros") %in%
+                        names(difference$Plots)))
+    for (plot in names(difference$Plots)) {
+        checkmate::expect_class(difference$Plots[[plot]], "ggplot")
+    }
+    expect_length(difference$QQPlots, 5)
+    expect_true(all(c("Means", "Variances", "LibrarySizes", "ZerosGene",
+                      "ZerosCell") %in% names(difference$QQPlots)))
+    for (plot in names(difference$QQPlots)) {
+        checkmate::expect_class(difference$QQPlots[[plot]], "ggplot")
+    }
+})
+
+# test_that("makeCompPanel works", {
+#     panel <- makeCompPanel(comparison)
+#     checkmate::expect_class(panel, "ggplot")
+# })
+#
+# test_that("makeDiffPanel works", {
+#     panel <- makeDiffPanel(difference)
+#     checkmate::expect_class(panel, "ggplot")
+# })
+#
+# test_that("makeOverallPanel works", {
+#     panel <- makeOverallPanel(comparison, difference)
+#     checkmate::expect_class(panel, "ggplot")
+# })
diff --git a/tests/testthat/test-listSims.R b/tests/testthat/test-listSims.R
new file mode 100644
index 0000000000000000000000000000000000000000..cf386c9437a04bcb0898e6cf633fc9e47a8aeab1
--- /dev/null
+++ b/tests/testthat/test-listSims.R
@@ -0,0 +1,10 @@
+context("listSims")
+
+test_that("listSims printing works", {
+    expect_output(listSims(), "Splatter currently contains")
+})
+
+test_that("listSims return works", {
+    ll <- listSims(print = FALSE)
+    checkmate::expect_class(ll, "data.frame")
+})
diff --git a/tests/testthat/test-lunEstimate.R b/tests/testthat/test-lunEstimate.R
new file mode 100644
index 0000000000000000000000000000000000000000..010ae358c0b9a825902f30e7d791e91abf409a7e
--- /dev/null
+++ b/tests/testthat/test-lunEstimate.R
@@ -0,0 +1,9 @@
+context("lunEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("lunEstimate works", {
+    params <- lunEstimate(sc_example_counts)
+    expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-phenoEstimate.R b/tests/testthat/test-phenoEstimate.R
new file mode 100644
index 0000000000000000000000000000000000000000..402d78164c1ad0e9491097aaa3cc978ab015e44d
--- /dev/null
+++ b/tests/testthat/test-phenoEstimate.R
@@ -0,0 +1,9 @@
+context("phenoEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("phenoEstimate works", {
+    params <- phenoEstimate(sc_example_counts)
+    expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-simpleEstimate.R b/tests/testthat/test-simpleEstimate.R
new file mode 100644
index 0000000000000000000000000000000000000000..3b581e1e25d09f87b79959934edcf82b6f93883f
--- /dev/null
+++ b/tests/testthat/test-simpleEstimate.R
@@ -0,0 +1,9 @@
+context("simpleEstimate")
+
+library(scater)
+data("sc_example_counts")
+
+test_that("simpleEstimate works", {
+    params <- simpleEstimate(sc_example_counts)
+    expect_true(validObject(params))
+})
diff --git a/tests/testthat/test-splat-simulate.R b/tests/testthat/test-splat-simulate.R
index 9d99cf7b7fc3c762d7a821a255c9ae6415ea87ad..d5b16f588beaa9f0d96499222a19b18298b71ff4 100644
--- a/tests/testthat/test-splat-simulate.R
+++ b/tests/testthat/test-splat-simulate.R
@@ -4,9 +4,11 @@ test.params <- newSplatParams(nGenes = 100, batchCells = c(5, 5),
                               group.prob = c(0.5, 0.5), lib.scale = 0)
 
 test_that("splatSimulate output is valid", {
-    expect_true(validObject(splatSimulate(test.params, method = "single")))
+    expect_true(validObject(splatSimulate(test.params, method = "single",
+                                          dropout.present = TRUE)))
     expect_true(validObject(splatSimulate(test.params, method = "groups")))
-    expect_true(validObject(splatSimulate(test.params, method = "paths")))
+    expect_true(validObject(splatSimulate(test.params, method = "paths",
+                                          path.from = c(0, 1))))
 })
 
 test_that("one group switches to single mode", {
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
new file mode 100644
index 0000000000000000000000000000000000000000..d4b7bdc9c180b44f901f5fcc17435e83755df90d
--- /dev/null
+++ b/tests/testthat/test-utils.R
@@ -0,0 +1,22 @@
+context("utils")
+
+test_that("logistic function works", {
+    expect_equal(logistic(0, x0 = 0, k = 1), 0.5)
+})
+
+test_that("rbindMatched works", {
+    df1 <- data.frame(A = 1:3, B = 4:6, C = 7:9)
+    df2 <- data.frame(D = 0)
+    expect_error(rbindMatched(df1, df2),
+                 "There must be at least two columns in common")
+    df2 <- data.frame(A = 1:3)
+    expect_error(rbindMatched(df1, df2),
+                 "There must be at least two columns in common")
+    df2 <- data.frame(A = 1:3, C = 7:9, D = 0)
+    expect_equal(colnames(rbindMatched(df1, df2)), c("A", "C"))
+})
+
+test_that("winsorize works", {
+    x <- c(0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2)
+    expect_true(all(winsorize(x, q = 0.1) == 1))
+})
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index ae895ee3c5d0c192fc358c541f32b2c67d383604..deae574400415ca390fbba2bc2584e2c6960dd27 100644
--- a/vignettes/splatter.Rmd
+++ b/vignettes/splatter.Rmd
@@ -36,7 +36,7 @@ biocLite("splatter")
 To install the most recent development version from Github use:
 
 ```{r install-github, eval = FALSE}
-biocLite("Oshlack/splatter", dependencies = TRUE, 
+biocLite("Oshlack/splatter", dependencies = TRUE,
          build_vignettes = TRUE)
 ```
 
@@ -51,6 +51,7 @@ Splatter. Here is an example using the example dataset in the `scater` package:
 library(splatter)
 
 # Load example data
+library(scater)
 data("sc_example_counts")
 # Estimate parameters from example data
 params <- splatEstimate(sc_example_counts)
@@ -160,7 +161,7 @@ As well as telling us what type of object we have ("A `Params` object of class
 some extra information. We can see which parameters can be estimated by the
 `splatEstimate` function (those in parentheses), which can't be estimated
 (those in brackets) and which have been changed from their default values (those
-in ALL CAPS). 
+in ALL CAPS).
 
 ## Getting and setting
 
@@ -330,7 +331,7 @@ So far we have only simulated a single population of cells but often we are
 interested in investigating a mixed population of cells and looking to see what
 cell types are present or what differences there are between them. Splatter is
 able to simulate these situations by changing the `method` argument Here we are
-going to simulate two groups, by specifying the `group.prob` parameter and 
+going to simulate two groups, by specifying the `group.prob` parameter and
 setting the `method` parameter to `"groups"`:
 
 (**NOTE:** We have also set the `verbose` argument to `FALSE` to stop Splatter
@@ -354,7 +355,7 @@ The other situation that is often of interest is a differentiation process where
 one cell type is changing into another. Splatter approximates this process by
 simulating a series of steps between two groups and randomly assigning each
 cell to a step. We can create this kind of simulation using the `"paths"`
-method. 
+method.
 
 ```{r paths}
 sim.paths <- splatSimulate(method = "paths", verbose = FALSE)
@@ -362,7 +363,7 @@ sim.paths <- normalise(sim.paths)
 plotPCA(sim.paths, colour_by = "Step")
 ```
 
-Here the colours represent the "step" of each cell or how far along the 
+Here the colours represent the "step" of each cell or how far along the
 differentiation path it is. We can see that the cells with dark colours are more
 similar to the originating cell type and the light coloured cells are closer
 to the final, differentiated, cell type. By setting additional parameters it is
@@ -462,9 +463,9 @@ tpm(sim)[1:5, 1:5]
 
 The default method used by `addGeneLengths` to simulate lengths is to generate
 values from a log-normal distribution which are then rounded to give an integer
-length. The parameters for this distribution are based on human protein coding 
-genes but can be adjusted if needed (for example for other species). 
-Alternatively lengths can be sampled from a provided vector (see 
+length. The parameters for this distribution are based on human protein coding
+genes but can be adjusted if needed (for example for other species).
+Alternatively lengths can be sampled from a provided vector (see
 `?addGeneLengths` for details and an example).
 
 # Comparing simulations and real data