diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2aed5bc..1c81026 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,19 +1,15 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
-      - devel
+    branches: [main, master, devel]
   pull_request:
-    branches:
-      - main
-      - master
-      - devel
+    branches: [main, master, devel]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -24,67 +20,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          #- {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
\ No newline at end of file
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 85ea3f7..27a9479 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -52,9 +52,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.0', bioc: '3.12'}
-          - { os: windows-latest, r: '4.0', bioc: '3.12'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          - { os: windows-latest, r: '4.4', bioc: '3.19'}
+          ## Check https://github.com/r-lib/actions/tree/master/examples
+          ## for examples using the http-user-agent
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -77,19 +79,20 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -97,28 +100,28 @@ jobs:
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-
 
-      - name: Install Linux system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
-          echo $sysreqs
-          sudo -s eval "$sysreqs"
+      # - name: Install Linux system dependencies
+      #   if: runner.os == 'Linux'
+      #   run: |
+      #     sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+      #     echo $sysreqs
+      #     sudo -s eval "$sysreqs"
 
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
@@ -137,6 +140,9 @@ jobs:
           ## For installing usethis's dependency gert
           brew install libgit2
 
+          ## Required for tcltk
+          brew install xquartz --cask
+
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |
@@ -151,7 +157,7 @@ jobs:
 
       - name: Set BiocVersion
         run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install dependencies pass 1
@@ -163,9 +169,13 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
+
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
         continue-on-error: true
         shell: Rscript {0}
 
@@ -173,12 +183,7 @@ jobs:
         run: |
           ## Pass #2 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
-
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          remotes::install_cran("rcmdcheck")
-          BiocManager::install("BiocCheck")
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics
@@ -189,13 +194,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Install pkgdown
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("pkgdown")
         shell: Rscript {0}
@@ -210,10 +215,12 @@ jobs:
       - name: Run CMD check
         env:
           _R_CHECK_CRAN_INCOMING_: false
+          DISPLAY: 99.0
         run: |
+          options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
-              args = c("--no-build-vignettes", "--no-manual", "--timings"),
-              build_args = c("--no-manual", "--no-resave-data"),
+              args = c("--no-manual", "--no-vignettes", "--timings"),
+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
               error_on = "warning",
               check_dir = "check"
           )
@@ -231,6 +238,8 @@ jobs:
         shell: Rscript {0}
 
       - name: Run BiocCheck
+        env:
+          DISPLAY: 99.0
         run: |
           BiocCheck::BiocCheck(
               dir('check', 'tar.gz$', full.names = TRUE),
@@ -241,40 +250,89 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
-          covr::codecov()
+          covr::codecov(coverage = covr::package_coverage(type = "all"))
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
-      - name: Deploy package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
-        shell: bash {0}
+      - name: Build pkgdown site
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
         ## at least one locally before this will work. This creates the gh-pages
         ## branch (erasing anything you haven't version controlled!) and
         ## makes the git history recognizable by pkgdown.
 
+      - name: Install deploy dependencies
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          apt-get update && apt-get -y install rsync
+
+      - name: Deploy pkgdown site to GitHub pages 🚀
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-results
           path: check
 
-      - uses: docker/build-push-action@v1
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
+
+  ## Code adapted from
+  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
+  docker-build-and-push:
+    runs-on: ubuntu-latest
+    needs: build-check
+    steps:
+      - name: Checkout Repository
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: actions/checkout@v3
+
+      - name: Register repo name
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        id: reg_repo_name
+        run: |
+          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
+
+      - name: Set up QEMU
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to Docker Hub
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
+      ## account, not your actual dockerhub account password. You can get it
+      ## from https://hub.docker.com/settings/security.
+      ## Check https://github.com/docker/build-push-action/tree/v4.0.0
+      ## for more details.
+      ## Alternatively, try checking
+      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
+
+      - name: Build and Push Docker
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
+        uses: docker/build-push-action@v4
         with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: pyanglab/cepo
-          tag_with_ref: true
-          tag_with_sha: true
-          tags: latest
+          context: .
+          push: true
+          tags: >
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 3c908d3..70ad1e3 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -1,48 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master, devel]
+  pull_request:
+    branches: [main, master, devel]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
index e27a888..6689a41 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Cepo
 Title: Cepo for the identification of differentially stable genes
-Version: 1.10.0
+Version: 1.10.2
 Authors@R: 
     c(
     person(given = "Hani Jieun",
@@ -19,7 +19,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1.9001
+RoxygenNote: 7.3.1
 Imports: 
     DelayedMatrixStats,
     DelayedArray,
@@ -35,7 +35,8 @@ Imports:
     reshape2,
     BiocParallel,
     stats,
-    dplyr
+    dplyr,
+    purrr
 biocViews: Classification, GeneExpression, SingleCell, Software, Sequencing, DifferentialExpression
 Suggests: 
     knitr,
@@ -48,8 +49,7 @@ Suggests:
     scMerge,
     fgsea,
     escape,
-    pheatmap,
-    patchwork
+    pheatmap
 VignetteBuilder: knitr
 Depends: 
     GSEABase,
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..813fa3d
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: Cepo authors
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..9842340
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 Cepo authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
index 77e8d11..e9ea0a6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -20,6 +20,8 @@ importFrom(grDevices,rainbow)
 importFrom(methods,is)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
+importFrom(purrr,map)
+importFrom(purrr,map2)
 importFrom(reshape2,melt)
 importFrom(rlang,.data)
 importFrom(stats,pchisq)
diff --git a/R/Cepo.R b/R/Cepo.R
index 436b84d..6eecf82 100644
--- a/R/Cepo.R
+++ b/R/Cepo.R
@@ -6,7 +6,7 @@
 #' Default to NULL to not remove any genes.
 #' @param prefilter_sd Numeric value indicating threshold relating to standard 
 #' deviation of genes. Used with prefilter_zeros. 
-#' @param prefilter_pzeros Numeric value indicating threshold relating to the 
+#' @param prefilter_pzero Numeric value indicating threshold relating to the 
 #' percentage of zero expression of genes. Used with prefilter_sd. 
 #' @param logfc Numeric value indicating the threshold of log fold-change 
 #' to use to filter genes.
@@ -39,6 +39,7 @@
 #' @importFrom HDF5Array HDF5Array
 #' @importFrom BiocParallel SerialParam MulticoreParam SnowParam bplapply
 #' @importFrom stats pnorm pchisq
+#' @importFrom purrr map map2
 #' @import dplyr
 #' @return Returns a list of key genes.
 #' @description ExprsMat accepts various matrix objects, 
@@ -52,7 +53,7 @@
 #' cepoOutput <- Cepo(logcounts(cellbench), cellbench$celltype)
 #' cepoOutput
 #' 
-Cepo <- function(exprsMat, cellTypes, minCells = 20, minCelltype = 3, exprsPct = NULL, 
+Cepo <- function(exprsMat, cellTypes, minCells = 20, minCelltype = 3, exprsPct = 0.05, 
                  prefilter_sd = NULL, prefilter_pzero = NULL,
                  logfc = NULL, computePvalue = NULL, computeFastPvalue = TRUE,
                  variability = "CV", method = "weightedMean",
@@ -258,8 +259,8 @@ bootFastCepo <- function(exprsMat, cellTypes, minCells, exprsPct, logfc, variabi
             this_celltype_stats_matrix = purrr::map(.x = sampled_cepo_stats, .f = function(this_sampled_stats){
                 this_sampled_stats[,this_celltype]
             }) %>% do.call(cbind, .)
-            this_celltype_stats_mean = Cepo:::rowMeans_withnames(this_celltype_stats_matrix)
-            this_celltype_stats_sd = Cepo:::rowSds_withnames(this_celltype_stats_matrix)
+            this_celltype_stats_mean = rowMeans_withnames(this_celltype_stats_matrix)
+            this_celltype_stats_sd = rowSds_withnames(this_celltype_stats_matrix)
             return(data.frame(mean = this_celltype_stats_mean, sd = this_celltype_stats_sd))
         })
     names(celltype_norm_stats) = cts
diff --git a/man/Cepo.Rd b/man/Cepo.Rd
index c3d3b2f..459bbcc 100644
--- a/man/Cepo.Rd
+++ b/man/Cepo.Rd
@@ -9,7 +9,7 @@ Cepo(
   cellTypes,
   minCells = 20,
   minCelltype = 3,
-  exprsPct = NULL,
+  exprsPct = 0.05,
   prefilter_sd = NULL,
   prefilter_pzero = NULL,
   logfc = NULL,
@@ -41,6 +41,9 @@ Default to NULL to not remove any genes.}
 \item{prefilter_sd}{Numeric value indicating threshold relating to standard
 deviation of genes. Used with prefilter_zeros.}
 
+\item{prefilter_pzero}{Numeric value indicating threshold relating to the
+percentage of zero expression of genes. Used with prefilter_sd.}
+
 \item{logfc}{Numeric value indicating the threshold of log fold-change
 to use to filter genes.}
 
@@ -71,9 +74,6 @@ For workers greater than 1, see the \code{workers} argument in
 
 \item{...}{Additional arguments passed to \code{BiocParallel::MulticoreParam}
 and \code{BiocParallel::SnowParam}.}
-
-\item{prefilter_pzeros}{Numeric value indicating threshold relating to the
-percentage of zero expression of genes. Used with prefilter_sd.}
 }
 \value{
 Returns a list of key genes.
diff --git a/vignettes/cepo.Rmd b/vignettes/cepo.Rmd
index 2821458..52c2b2b 100644
--- a/vignettes/cepo.Rmd
+++ b/vignettes/cepo.Rmd
@@ -18,6 +18,10 @@ We introduce *Cepo*, a method to determine genes governing cell identity from sc
 
 *Cepo* is therefore distinct from most methods for differential analysis (e.g., differential expression) that prioritise differences in the mean abundance between cell types. *Cepo* is able to capture subtle variations in distribution that does not necessarily involve changes in mean. *Cepo* is particularly suitable for large atlas data as it is computationally efficient and fast. Moreover, *Cepo* can perform differential stability analysis for multi-group comparisons in single-cell data.
 
+```{r, include = FALSE}
+knitr::opts_chunk$set(crop = NULL)
+```
+
 To access the R code used in the vignettes, type:
 ```
 browseVignettes("Cepo")
@@ -283,9 +287,8 @@ We can also perform a plethora of downstream analyses, from gene set enrichment
 ```{r gsea, message = FALSE}
 library(escape)
 library(fgsea)
-hallmark <- getGeneSets(species = "Homo sapiens", 
+hallmarkList <- getGeneSets(species = "Homo sapiens", 
                            library = "H")
-hallmarkList <- geneIds(hallmark)
 
 fgseaRes <- fgsea(pathways = hallmarkList, 
                   stats    = sort(ds_res_batches$average$stats[,"beta"]),
@@ -303,8 +306,8 @@ enriched_beta[1:5]
 
 Finally, we can visualise the enrichment using the `plotEnrichment` function from the `fgsea` package.
 ```{r fig.height=5, fig.width=5}
-plotEnrichment(hallmarkList[["HALLMARK_PANCREAS_BETA_CELLS"]],
-               sort(ds_res_batches$average$stats[, "beta"])) + labs(title="HALLMARK_PANCREAS_BETA_CELLS")
+plotEnrichment(hallmarkList[["HALLMARK-PANCREAS-BETA-CELLS"]],
+               sort(ds_res_batches$average$stats[, "beta"])) + labs(title="HALLMARK-PANCREAS-BETA-CELLS")
 ```