diff --git a/.Rbuildignore b/.Rbuildignore
index a087f76231d83b5bbee2580d2b3b2b2105b6bd52..5c7dbad65f33379850f6c86bc7b0c8cde6549c57 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,5 +6,6 @@
 ^NEWS\.md$
 ^\.git*
 ^docs$
+^index\.md$
 ^_pkgdown\.yml$
 ^pkgdown$
diff --git a/DESCRIPTION b/DESCRIPTION
index 304ab01523ae5364fc9bd2a3f164f849e15040b6..bd992ad20a79311e95a15489630930fd4eaeaa7d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,36 +21,37 @@ License: GPL-3 + file LICENSE
 LazyData: TRUE
 Depends:
     R (>= 3.4),
-    scater
+    scater,
+    SingleCellExperiment
 Imports:
-    fitdistrplus,
-    edgeR,
-    stats,
-    locfit,
     akima,
-    Biobase,
+    BiocGenerics,
+    BiocParallel,
     checkmate,
-    methods,
-    utils,
-    matrixStats,
+    edgeR,
+    fitdistrplus,
     ggplot2,
+    locfit,
+    matrixStats,
+    methods,
     scales,
-    BiocParallel,
-    SummarizedExperiment
+    stats,
+    SummarizedExperiment,
+    utils
 Suggests:
-    testthat,
-    scran,
-    progress,
+    BiocStyle,
+    covr,
+    cowplot,
+    knitr,
+    limSolve,
     lme4,
+    progress,
     pscl,
-    scDD,
-    knitr,
+    testthat,
     rmarkdown,
-    BiocStyle,
-    covr,
     S4Vectors,
-    cowplot,
-    limSolve
+    scDD,
+    scran
 biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
     Software
 URL: https://github.com/Oshlack/splatter
diff --git a/R/lun2-simulate.R b/R/lun2-simulate.R
index 21e3cdb56369fafa82baecfa6f018555ee90757a..35329de75e4dd9f9fff1fb643c349e475c8997b4 100644
--- a/R/lun2-simulate.R
+++ b/R/lun2-simulate.R
@@ -137,7 +137,7 @@ lun2Simulate <- function(params = newLun2Params(), zinb = FALSE,
         plate.means[, ingroup] <- plate.means[, ingroup] * de.facs
         plate.means[, -ingroup] <- plate.means[, -ingroup] * (1 / de.facs)
 
-        phenos$Ingroup <- cell.plates %in% plate.ingroup
+        cells$Ingroup <- cell.plates %in% plate.ingroup
         features$DEFacIngroup <- de.facs
         features$DEFacOutgroup <- 1 / de.facs
         for (idx in seq_len(nPlates)) {
diff --git a/R/splat-simulate.R b/R/splat-simulate.R
index 6684d2321b31a59efb058d1b88e9a49afa7ef906..98dd989939ca7aa147716f880fea1c2850dae8b4 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -100,8 +100,8 @@
 #'
 #' @examples
 #' # Simulation with default parameters
-#' \dontrun{
 #' sim <- splatSimulate()
+#' \dontrun{
 #' # Simulation with different number of genes
 #' sim <- splatSimulate(nGenes = 1000)
 #' # Simulation with custom parameters
@@ -699,7 +699,7 @@ splatSimDropout <- function(sim, params) {
         nGenes <- getParam(params, "nGenes")
         dropout.mid <- getParam(params, "dropout.mid")
         dropout.shape <- getParam(params, "dropout.shape")
-        cell.means <- get_exprs(sim, "CellMeans")
+        cell.means <- assays(sim)$CellMeans
 
         # Generate probabilites based on expression
         drop.prob <- sapply(seq_len(nCells), function(idx) {
@@ -724,7 +724,7 @@ splatSimDropout <- function(sim, params) {
         counts <- true.counts
     }
 
-    counts(sim) <- counts
+    BiocGenerics::counts(sim) <- counts
 
     return(sim)
 }
diff --git a/man/splatSimulate.Rd b/man/splatSimulate.Rd
index 0db1f7205a0264e5b164c796fc2814dc27ea0120..1b06a3f563ffccf97a3cf3f193bb78cb08b66826 100644
--- a/man/splatSimulate.Rd
+++ b/man/splatSimulate.Rd
@@ -115,8 +115,8 @@ which typically use \code{underscore_naming}.
 }
 \examples{
 # Simulation with default parameters
-\dontrun{
 sim <- splatSimulate()
+\dontrun{
 # Simulation with different number of genes
 sim <- splatSimulate(nGenes = 1000)
 # Simulation with custom parameters