diff --git a/.Rbuildignore b/.Rbuildignore
index ed74521..6c3acff 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -5,3 +5,5 @@
 ^CODE_OF_CONDUCT\.md$
 TODO.md$
 ^\.github$
+^\.positai$
+^\.claude$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index ed58530..f10f90f 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.21'}
-          - { os: windows-latest, r: 'devel', bioc: '3.21'}
+          - { os: ubuntu-latest, r: 'release', bioc: '3.24', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: 'release', bioc: '3.24'}
+          - { os: windows-latest, r: 'release', bioc: '3.24'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
diff --git a/DESCRIPTION b/DESCRIPTION
index c79776b..7ec156d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -28,7 +28,8 @@ Suggests:
     knitr,
     rmarkdown,
     BiocStyle,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    scrapper
 URL: https://github.com/iSEE/iSEEid
 BugReports: https://github.com/iSEE/iSEEid/issues
 VignetteBuilder: knitr
diff --git a/R/panel_SampleIdentificationCenter.R b/R/panel_SampleIdentificationCenter.R
index 102da6f..7b4425c 100644
--- a/R/panel_SampleIdentificationCenter.R
+++ b/R/panel_SampleIdentificationCenter.R
@@ -23,17 +23,7 @@
 #' @return A panel designed to work within the iSEE framework
 #'
 #' @aliases
-#' SampleIdentificationCenter SampleIdentificationCenter-class
-#' .createObservers,SampleIdentificationCenter-method
-#' .defineDataInterface,SampleIdentificationCenter-method
-#' .defineOutput,SampleIdentificationCenter-method
-#' .definePanelTour,SampleIdentificationCenter-method
-#' .fullName,SampleIdentificationCenter-method
-#' .generateOutput,SampleIdentificationCenter-method
-#' .multiSelectionResponsive,SampleIdentificationCenter-method
-#' .panelColor,SampleIdentificationCenter-method
-#' .renderOutput,SampleIdentificationCenter-method
-#' initialize,SampleIdentificationCenter-method
+#' SampleIdentificationCenter SampleIdentificationCenter-class .createObservers,SampleIdentificationCenter-method .defineDataInterface,SampleIdentificationCenter-method .defineOutput,SampleIdentificationCenter-method .definePanelTour,SampleIdentificationCenter-method .fullName,SampleIdentificationCenter-method .generateOutput,SampleIdentificationCenter-method .multiSelectionResponsive,SampleIdentificationCenter-method .panelColor,SampleIdentificationCenter-method .renderOutput,SampleIdentificationCenter-method initialize,SampleIdentificationCenter-method
 #'
 #' @examples
 #' library(iSEE)
@@ -44,7 +34,8 @@
 #' class(sce)
 #'
 #' library(scater)
-#' sce <- logNormCounts(sce, exprs_values = "tophat_counts")
+#' library(scrapper)
+#' sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
 #'
 #' sce <- runPCA(sce, ncomponents=4)
 #' sce <- runTSNE(sce)
diff --git a/README.Rmd b/README.Rmd
index bc32fbd..9fd99a9 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -50,9 +50,10 @@ library("iSEEid")
 library("iSEE")
 library("scRNAseq")
 library("scater")
+library("scrapper")
 
 sce <- ReprocessedAllenData(assays = "tophat_counts")
-sce <- logNormCounts(sce, exprs_values = "tophat_counts")
+sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
 sce <- runPCA(sce, ncomponents = 4)
 sce <- runTSNE(sce)
 
diff --git a/README.md b/README.md
index 76644d2..1546e59 100644
--- a/README.md
+++ b/README.md
@@ -44,9 +44,10 @@ library("iSEEid")
 library("iSEE")
 library("scRNAseq")
 library("scater")
+library("scrapper")
 
 sce <- ReprocessedAllenData(assays = "tophat_counts")
-sce <- logNormCounts(sce, exprs_values = "tophat_counts")
+sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
 sce <- runPCA(sce, ncomponents = 4)
 sce <- runTSNE(sce)
 
diff --git a/man/SampleIdentificationCenter-class.Rd b/man/SampleIdentificationCenter-class.Rd
index 7b90988..6ec11af 100644
--- a/man/SampleIdentificationCenter-class.Rd
+++ b/man/SampleIdentificationCenter-class.Rd
@@ -52,7 +52,8 @@ sce <- ReprocessedAllenData(assays = "tophat_counts")
 class(sce)
 
 library(scater)
-sce <- logNormCounts(sce, exprs_values = "tophat_counts")
+library(scrapper)
+sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
 
 sce <- runPCA(sce, ncomponents=4)
 sce <- runTSNE(sce)
diff --git a/vignettes/Introduction_to_iSEEid.Rmd b/vignettes/Introduction_to_iSEEid.Rmd
index e091e65..e3e03a3 100644
--- a/vignettes/Introduction_to_iSEEid.Rmd
+++ b/vignettes/Introduction_to_iSEEid.Rmd
@@ -81,9 +81,10 @@ library("iSEE")
 library("iSEEid")
 library("scRNAseq")
 library("scater")
+library("scrapper")
 
 sce <- ReprocessedAllenData(assays = "tophat_counts")
-sce <- logNormCounts(sce, exprs_values = "tophat_counts")
+sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
 sce <- runPCA(sce, ncomponents = 4)
 sce <- runTSNE(sce)