diff --git a/.github/package-versions.txt b/.github/package-versions.txt
new file mode 100644
index 0000000..2facfd9
--- /dev/null
+++ b/.github/package-versions.txt
@@ -0,0 +1 @@
+any::Seurat@4.1.1, any::Matrix@1.5.1
\ No newline at end of file
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 07d305f..d53b9fb 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, dev, DEV]
+    branches: [ main, master, dev, DEV ]
   pull_request:
-    branches: [main, master, dev, DEV]
+    branches: [ main, master, dev, DEV ]
   workflow_dispatch:
 
 name: R-CMD-check
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.1.3' }
+          - { os: ubuntu-latest, r: "4.1.3" }
           #- { os: ubuntu-latest, r: 'oldrel-1' }
           #- { os: macos-latest, r: 'release' }
     runs-on: ${{ matrix.config.os }}
@@ -27,27 +27,32 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-    container:
-      image: nciccbr/scworkflow:v1.0.2_79e5d37
     steps:
       - uses: actions/checkout@v4
-      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - uses: CCBR/actions/install-r-pak@main
         with:
+          versions-file: .github/package-versions.txt
           extra-packages: local::.
           needs: dev
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
 
   lint:
     runs-on: ubuntu-latest
-    container:
-      image: nciccbr/scworkflow:v1.0.2_79e5d37
     steps:
       - uses: actions/checkout@v4
-      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - uses: CCBR/actions/install-r-pak@main
         with:
+          r-version: 4.1.3
+          versions-file: .github/package-versions.txt
           needs: dev
+
       - name: Good Practice checks
         shell: Rscript {0}
         run: |
@@ -103,11 +108,12 @@ jobs:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
 
-  check: # make sure all check jobs pass. https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+  check:
+    # make sure all check jobs pass. https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
     runs-on: ubuntu-latest
     container:
       image: nciccbr/scworkflow:v1.0.2_79e5d37
-    needs: [R-CMD-check, lint, test-coverage]
+    needs: [ R-CMD-check, lint, test-coverage ]
     if: always()
     steps:
       - name: Successful build
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 9e96b07..a6822bc 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -56,4 +56,4 @@ jobs:
             BUILD_DATE=${{ steps.vars.outputs.DATE }}
             BUILD_TAG=${{ steps.vars.outputs.VERSION_TAG }}
             REPONAME=${{ env.IMAGE_NAME }}
-            R_VERSION=4.3.2
+            R_VERSION=4.1.3
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index e5b2def..33b9b71 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -2,11 +2,11 @@
 # 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 ]
   pull_request:
-    branches: [main, master]
+    branches: [ main, master ]
   release:
-    types: [published]
+    types: [ published ]
   workflow_dispatch:
 
 name: pkgdown
@@ -27,9 +27,10 @@ jobs:
       image: nciccbr/scworkflow:v1.0.2_79e5d37
     steps:
       - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: CCBR/actions/install-r-pak@main
         with:
+          r-version: 4.1.3
+          versions-file: .github/package-versions.txt
           extra-packages: local::.
           needs: dev
 
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..4ac1c43
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,58 @@
+# 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, dev, DEV]
+  pull_request:
+    branches: [main, master, dev, DEV]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: CCBR/actions/install-r-pak@main
+        with:
+          r-version: 4.1.3
+          versions-file: .github/package-versions.txt
+          needs: dev
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
index 314834f..f2fa164 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,10 +9,10 @@ tests/testthat/fixtures/
 tests/testthat/output/
 
 .Rproj.user
-
 inst/doc
 /doc/
 /Meta/
 
 .github.zip
 decision_log.md
+
diff --git a/DESCRIPTION b/DESCRIPTION
index 4efee31..ed084e5 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -34,7 +34,6 @@ Imports:
     callr (>= 3.7.1),
     celldex,
     colorspace,
-    colorspace,
     ComplexHeatmap (>= 2.10.0),
     cowplot (>= 1.1.1),
     data.table (>= 1.14.2),
@@ -52,23 +51,45 @@ Imports:
     ggplot2 (>= 3.3.6),
     ggpubr (>= 0.4.0),
     ggrepel,
+    globals (>= 0.16.1),
     gridBase (>= 0.4-7),
     gridExtra (>= 2.3),
     gtable (>= 0.3.1),
+    harmony (>= 0.1.1),
+    hdf5r (>= 1.3.5),
     htmlwidgets,
+    httpuv (>= 1.6.5),
     httr,
     jsonlite,
+    leiden (>= 0.4.2),
+    limma (>= 3.50.3),
+    magrittr (>= 2.0.3),
+    markdown (>= 1.1),
     MAST (>= 1.20.0),
-    patchwork,
+    methods (>= 4.1.3),
     pheatmap,
+    plotly (>= 4.10.0),
     plyr,
     png,
+    progressr (>= 0.10.1),
+    purrr (>= 0.3.4),
+    quantmod (>= 0.4.20),
     RColorBrewer (>= 1.1-3),
+    reshape2 (>= 1.4.4),
+    reticulate (>= 1.25),
+    rlang (>= 1.0.6),
     scales,
     scDblFinder,
     Seurat (>= 4.1.1),
     SingleR (>= 1.8.1),
+    statmod (>= 1.4.37),
+    stringr (>= 1.4.1),
+    svglite (>= 2.1.0),
+    tibble (>= 3.1.8),
     tidyr,
+    tidyverse (>= 1.3.2),
+    viridisLite (>= 0.4.0),
+    xfun (>= 0.32),
     zip (>= 2.2.0)
 Suggests:
     knitr,
diff --git a/Dockerfile b/Dockerfile
index 0d61765..9a4b171 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -26,24 +26,87 @@ RUN conda config --add channels conda-forge \
  && conda config --set channel_priority strict
 
 # install conda packages
-RUN mamba install -y -c conda-forge \
+# Note: Most version pins removed to allow conda to resolve compatible versions with R 4.1.3
+# Only R version is pinned per requirement
+RUN mamba install -y \
     r-base=${R_VERSION} \
-    r-devtools \
+    r-anndata \
+    r-biocmanager \
+    r-callr \
+    bioconductor-celldex \
+    r-colorspace \
+    bioconductor-complexheatmap \
+    r-cowplot \
+    r-data.table \
+    r-dendextend \
+    r-dendsort \
+    r-digest \
+    r-dplyr \
+    bioconductor-edger \
+    r-future \
+    r-future.apply \
+    r-gargle \
+    r-gdata \
+    r-ggextra \
     r-ggplot2 \
-    r-ggrepel r-viridis r-upsetr r-patchwork r-plotly \
-    r-matrix r-mgcv r-survival \
-    bioconductor-genomicranges \
-    bioconductor-summarizedexperiment \
-    bioconductor-delayedarray \
-    bioconductor-s4arrays \
-    bioconductor-annotationdbi \
-    bioconductor-annotate \
-    bioconductor-keggrest \
+    r-ggpubr \
+    r-ggrepel \
+    r-globals \
+    r-gridbase \
+    r-gridextra \
+    r-gtable \
+    r-harmony \
+    r-hdf5r \
+    r-htmlwidgets \
+    r-httpuv \
+    r-httr \
+    r-jsonlite \
+    r-leiden \
+    bioconductor-limma \
+    r-magrittr \
+    r-markdown \
+    bioconductor-mast \
+    r-pheatmap \
+    r-plotly \
+    r-plyr \
+    r-png \
+    r-progressr \
+    r-purrr \
+    r-quantmod \
+    r-rcolorbrewer \
+    r-reshape2 \
+    r-reticulate \
+    r-rlang \
+    r-scales \
+    bioconductor-scdblfinder \
+    r-seurat=4.1.1 \
+    bioconductor-singler \
+    r-statmod \
+    r-stringr \
+    r-svglite \
+    r-tibble \
+    r-tidyr \
+    r-tidyverse \
+    r-viridislite \
+    r-xfun \
+    r-zip \
+    r-knitr \
+    r-rmarkdown \
+    r-roxygen2 \
+    r-testthat \
+    r-usethis \
+    r-cffr \
+    r-covr \
+    r-goodpractice \
+    r-here \
+    r-lintr \
+    r-pkgdown \
+    r-rcmdcheck \
   && conda clean -afy
 
 # install R package
 COPY . /opt2/SCWorkflow
-RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, repos='http://cran.rstudio.com')"
+RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, upgrade = 'never', repos='http://cran.rstudio.com')"
 
 # add scworkflow exec to the path
 # RUN chmod -R +x /opt2/conda/lib/R/library/SCWorkflow/exec
@@ -51,14 +114,51 @@ RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, repos
 # RUN scworkflow --help
 
 # copy example script & json to data
-COPY ./inst/extdata/example_script.sh /data2/
-COPY ./inst/extdata/json_args/ /data2/json_args/
+# COPY ./inst/extdata/example_script.sh /data2/
+# COPY ./inst/extdata/json_args/ /data2/json_args/
 
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 
+# Verify all dependencies from DESCRIPTION are installed
+RUN cat > /tmp/check_description_deps.R << 'EOF'
+# Parse DESCRIPTION file and check if all dependencies are installed
+desc_file <- "/opt2/SCWorkflow/DESCRIPTION"
+if (!file.exists(desc_file)) {
+  stop("DESCRIPTION file not found at ", desc_file)
+}
+# Read and parse DESCRIPTION
+desc <- read.dcf(desc_file)
+# Extract dependencies
+extract_packages <- function(str) {
+  if (is.na(str) || str == "") return(character(0))
+  # Split by comma and clean up whitespace and version specs
+  pkgs <- strsplit(str, ",")[[1]]
+  pkgs <- trimws(pkgs)
+  pkgs <- gsub("\\s*\\(.*\\)$", "", pkgs)  # Remove version specs
+  pkgs <- pkgs[pkgs != ""]
+  pkgs
+}
+deps <- unique(c(
+  extract_packages(desc[1, "Depends"]),
+  extract_packages(desc[1, "Imports"]),
+  extract_packages(desc[1, "Suggests"]),
+  extract_packages(desc[1, "Config/Needs/dev"])
+))
+# Remove base R
+deps <- deps[!grepl("^R$", deps)]
+# Check if each dependency is installed
+missing <- deps[!vapply(deps, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1))]
+if (length(missing) > 0) {
+  stop("The following dependencies are missing: ", paste(missing, collapse = ", "))
+} else {
+  message("All dependencies are installed.")
+}
+EOF
+RUN R --vanilla --slave --file=/tmp/check_description_deps.R
+
 # cleanup
 WORKDIR /data2
 RUN apt-get clean && apt-get purge \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
\ No newline at end of file
diff --git a/Dockerfile.rs413s b/Dockerfile.rs413s
new file mode 100644
index 0000000..e957f2a
--- /dev/null
+++ b/Dockerfile.rs413s
@@ -0,0 +1,548 @@
+FROM rocker/rstudio:4.1.3
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+      bash gcc g++ gfortran make cmake pkg-config \
+      git vim-tiny \
+      libcurl4-openssl-dev libssl-dev libxml2-dev \
+      libpng-tools \
+      libpng-dev libjpeg-dev libtiff5-dev zlib1g-dev \
+      libfreetype6-dev libharfbuzz-dev libfribidi-dev \
+      libbz2-dev liblzma-dev \
+      libgsl-dev libhdf5-dev \
+      tcl tk tcl-dev tk-dev \
+      libglpk-dev libglpk40 \
+      libgit2-dev \
+      python3 python3-venv \
+      python3-dev python3-pip \
+      libfontconfig1-dev \
+      autoconf automake libtool \
+      libgeos-dev libproj-dev \
+      libcairo2-dev libxt-dev \
+      automake \
+    && rm -rf /var/lib/apt/lists/*
+
+
+#      libpng libtiff-4 libjpeg libwebp libwebpmux 
+
+# (Optional) prevent R networking during local install steps
+# xxx rpf get rid of
+# RUN echo 'options(repos = c())' >> /usr/local/lib/R/etc/Rprofile.site
+
+#RUN pip3 install --no-cache-dir igraph leidenalg numpy
+# weird pip instal bug introduced 
+RUN pip3 install --no-cache-dir igraph "leidenalg==0.10.0" numpy
+
+WORKDIR /home/rstudio
+
+# Remove any spatstat* that might be preinstalled in the rocker image
+RUN R -q -e " \
+  for (lib in .libPaths()) { \
+    ip <- rownames(installed.packages(lib.loc = lib)); \
+    pk <- grep('^spatstat', ip, value = TRUE); \
+    if (length(pk)) { \
+      message('Removing from ', lib, ': ', paste(pk, collapse=', ')); \
+      remove.packages(pk, lib = lib); \
+    } \
+  }"
+
+# Install packages with specific versions from CRAN and Bioconductor
+RUN R --vanilla --slave << 'EOF'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+
+if (!require('BiocManager', quietly = TRUE)) {
+  install.packages('BiocManager', quiet = TRUE)
+}
+if (!require('remotes', quietly = TRUE)) {
+  install.packages('remotes', quiet = TRUE)
+}
+
+# Install specific CRAN package versions
+cran_versions <- list(
+  bitops = '1.0-8',
+  RCurl = '1.98-1.14',
+  GlobalOptions = '0.1.2',
+  bit = '4.0.4',
+  assertthat = '0.2.1',
+  bit64 = '4.0.5',
+  shape = '1.4.6',
+  colorspace = '2.0-3',
+  circlize = '0.4.15',
+  rlang = '1.1.4',
+  cli = '3.6.3',
+  glue = '1.7.0',
+  lifecycle = '1.0.4',
+  vctrs = '0.6.5',
+  blob = '1.2.3',
+  clue = '0.3-61',
+  cluster = '2.1.2',
+  codetools = '0.2-18',
+  crayon = '1.5.3',
+  data.table = '1.15.4',
+  DBI = '1.2.3',
+  dendsort = '0.3.4',
+  digest = '0.6.37',
+  ellipsis = '0.3.2',
+  evaluate = '0.24.0',
+  fansi = '1.0.6',
+  farver = '2.1.1',
+  fastmap = '1.2.0',
+  cachem = '1.1.0',
+  fastmatch = '1.1-3',
+  iterators = '1.0.14',
+  foreach = '1.5.2',
+  formatR = '1.14',
+  generics = '0.1.3',
+  rjson = '0.2.21',
+  GetoptLong = '1.0.5',
+  gtable = '0.3.5',
+  labeling = '0.4.2',
+  munsell = '0.5.0',
+  R6 = '2.5.1',
+  gridExtra = '2.3',
+  RColorBrewer = '1.1-3',
+  utf8 = '1.2.4',
+  pillar = '1.9.0',
+  pkgconfig = '2.0.3',
+  viridisLite = '0.4.1',
+  scales = '1.2.1',
+  withr = '3.0.1',
+  gtools = '3.9.5',
+  gridGraphics = '0.5-1',
+  hms = '1.1.2',
+  irlba = '2.3.5.1',
+  jsonlite = '1.8.8',
+  png = '0.1-7',
+  KernSmooth = '2.23-20',
+  lambda.r = '1.2.4',
+  lattice = '0.20-45',
+  lazyeval = '0.2.2',
+  locfit = '1.5-9.9',
+  Matrix = '1.5-1',
+  matrixStats = '0.62.0',
+  memoise = '2.0.1',
+  mgcv = '1.8-39',
+  nlme = '3.1-155',
+  rsvd = '1.0.5',
+  Rcpp = '1.0.13',
+  uuid = '1.1-0',
+  xfun = '0.47',
+  xtable = '1.8-4',
+  yaml = '2.3.10',
+  beeswarm = '0.4.0',
+  filelock = '1.0.3',
+  bslib = '0.4.2',
+  Cairo = '1.6-0',
+  desc = '1.4.2',
+  pkgload = '1.3.0',
+  brio = '1.1.3',
+  zip = '2.3.3',
+  openxlsx = '4.2.5.2',
+  praise = '1.0.0',
+  diffobj = '0.3.5',
+  waldo = '0.5.1',
+  testthat = '3.1.6',
+  nloptr = '2.0.3',
+  minqa = '1.2.5',
+  lme4 = '1.1-33',
+  MatrixModels = '0.5-1',
+  SparseM = '1.81',
+  quantreg = '5.95',
+  numDeriv = '2016.8-1.1',
+  pbkrtest = '0.5.2',
+  maptools = '1.1-7',
+  carData = '3.0-5',
+  rio = '0.5.29',
+  car = '3.0-0',
+  pROC = '1.18.2',
+  proxy = '0.4-27',
+  e1071 = '1.7-13',
+  ModelMetrics = '1.2.2.2',
+  clock = '0.7.0',
+  shinyjs = '2.1.0',
+  colourpicker = '1.2.0',
+  combinat = '0.0-8',
+  corrplot = '0.92',
+  cpp11 = '0.4.7',
+  diagram = '1.6.5',
+  DT = '0.28',
+  Rttf2pt1 = '1.3.12',
+  extrafontdb = '1.0',
+  extrafont = '0.18',
+  vipor = '0.4.7',
+  ggbeeswarm = '0.7.2',
+  ggrastr = '1.0.2',
+  fastICA = '1.2-3',
+  gdata = '2.18.0.1',
+  ggExtra = '0.10.1',
+  ggsci = '3.0.0',
+  ggsignif = '0.6.3',
+  gower = '1.0.1',
+  gridBase = '0.4-7',
+  hardhat = '1.3.0',
+  RhpcBLASctl = '0.23-42',
+  hdf5r = '1.3.5',
+  hexbin = '1.28.3',
+  survival = '3.2-13',
+  MASS = '7.3-55',
+  SQUAREM = '2021.1',
+  lava = '1.7.2.1',
+  lobstr = '1.1.2',
+  lsei = '1.3-0',
+  markdown = '1.13',
+  lpSolve = '5.6.16',
+  mclust = '6.0.0',
+  npsurv = '0.5-0',
+  pheatmap = '1.0.12',
+  polynom = '1.4-1',
+  proj4 = '1.0-12',
+  pryr = '0.1.5',
+  ps = '1.8.1',
+  RcppParallel = '5.1.6',
+  rstatix = '0.7.0',
+  timeDate = '4022.108',
+  maps = '3.4.1',
+  ggpubr = '0.4.0',
+  prodlim = '2023.03.31',
+  ipred = '0.9-14',
+  recipes = '1.0.6',
+  caret = '6.0-94',
+  quantmod = '0.4.20',
+  profvis = '0.3.7',
+  sessioninfo = '1.2.3',
+  downlit = '0.4.2',
+  whisker = '0.4.1',
+  pkgdown = '2.0.7',
+  pkgbuild = '1.4.8',
+  brew = '1.0-8',
+  roxygen2 = '7.2.3',
+  urlchecker = '1.0.1',
+  rversions = '2.1.2',
+  xopen = '1.0.0',
+  rcmdcheck = '1.4.0',
+  credentials = '1.3.2',
+  gert = '1.9.2',
+  gitcreds = '0.1.2',
+  httr2 = '0.2.3',
+  ini = '0.3.1',
+  gh = '1.4.0',
+  usethis = '3.1.0',
+  devtools = '2.4.5',
+  ggalt = '0.4.0',
+  EnhancedVolcano = '1.12.0'
+)
+
+for (pkg in names(cran_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = cran_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version failed for ', pkg, ', trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+
+# Install Bioconductor packages with specific versions
+bioc_versions <- list(
+  BiocGenerics = '0.40.0',
+  Biobase = '2.54.0',
+  S4Vectors = '0.32.4',
+  IRanges = '2.28.0',
+  XVector = '0.34.0',
+  GenomeInfoDbData = '1.2.7',
+  GenomeInfoDb = '1.30.1',
+  beachmat = '2.10.0',
+  edgeR = '3.36.0',
+  GenomicRanges = '1.46.1',
+  Biostrings = '2.62.0',
+  DelayedArray = '0.20.0',
+  sparseMatrixStats = '1.6.0',
+  DelayedMatrixStats = '1.16.0',
+  ScaledMatrix = '1.2.0',
+  zlibbioc = '1.40.0',
+  KEGGREST = '1.34.0',
+  AnnotationDbi = '1.56.2',
+  BiocParallel = '1.28.3',
+  BiocSingular = '1.10.0',
+  ComplexHeatmap = '2.10.0',
+  fgsea = '1.20.0',
+  BiocNeighbors = '1.12.0',
+  BiocFileCache = '2.2.1',
+  bluster = '1.4.0',
+  scuttle = '1.4.0',
+  scater = '1.22.0',
+  scran = '1.22.1',
+  SingleR = '1.8.1',
+  MAST = '1.20.0',
+  scDblFinder = '1.8.0',
+  SummarizedExperiment = '1.24.0',
+  SingleCellExperiment = '1.16.0',
+  HDF5Array = '1.22.1',
+  rhdf5 = '2.38.1',
+  rhdf5filters = '1.6.0',
+  GSVA = '1.42.0',
+  ExperimentHub = '2.2.1',
+  AnnotationHub = '3.2.2',
+  celldex = '1.4.0',
+  annotate = '1.72.0',
+  graph = '1.72.0',
+  GSEABase = '1.56.0',
+  interactiveDisplayBase = '1.32.0',
+  TrajectoryUtils = '1.2.0',
+  TSCAN = '1.32.0',
+  conquer = '1.3.3',
+  metapod = '1.2.0',
+  statmod = '1.5.0'
+)
+
+for (pkg in names(bioc_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = bioc_versions[[pkg]], repos = BiocManager::repositories(), quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version failed for ', pkg, ', trying BiocManager')
+    BiocManager::install(pkg, ask = FALSE, quiet = TRUE)
+  })
+}
+EOF
+
+
+# Additional packages that need special installation
+
+# Install SCWorkflow from GitHub
+COPY . /opt/SCWorkflow
+RUN R --vanilla --slave -e "remotes::install_local('/opt/SCWorkflow', dependencies = TRUE, quiet = TRUE, upgrade='never')"
+
+# Install spatstat family packages with specific versions
+RUN cat > /tmp/install_spatstat.R << 'EOFSPAT'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+if (!require('remotes', quietly = TRUE)) install.packages('remotes', quiet = TRUE)
+spatstat_versions <- list(
+  spatstat.utils = '3.1-0',
+  spatstat.data = '3.0-0',
+  deldir = '2.0-4',
+  polyclip = '1.10-7',
+  spatstat.univar = '2.0-3',
+  spatstat.geom = '3.0-3',
+  spatstat.random = '2.2-0',
+  abind = '1.4-5',
+  tensor = '1.5',
+  goftest = '1.2-3',
+  spatstat.sparse = '3.1-0',
+  spatstat.core = '2.4-2',
+  spatstat.linnet = '2.2-1'
+)
+for (pkg in names(spatstat_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = spatstat_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version for ', pkg, ' failed, trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+EOFSPAT
+
+RUN R --vanilla --slave --file=/tmp/install_spatstat.R
+
+# Install remaining specialized packages
+RUN cat > /tmp/install_special.R << 'EOFSPEC'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+if (!require('remotes', quietly = TRUE)) install.packages('remotes', quiet = TRUE)
+special_versions <- list(
+  RSpectra = '0.16-1',
+  dotCall64 = '1.1-1',
+  spam = '2.11-0',
+  RcppHNSW = '0.4.1',
+  leidenbase = '0.1.30',
+  fastDummies = '1.7.3',
+  sp = '1.5-0',
+  rgeos = '0.5-9',
+  SeuratObject = '4.1.1',
+  Seurat = '4.1.1',
+  XML = '3.99-0.14',
+  anndata = '0.7.5.2',
+  ash = '1.0-15',
+  viridis = '0.6.5',
+  dendextend = '1.16.0',
+  ggrepel = '0.9.5',
+  l2p = '0.0-13',
+  l2psupp = '0.0-13',
+  ica = '1.0-3',
+  Rtsne = '0.16',
+  ggridges = '0.5.3',
+  scattermore = '1.2',
+  listenv = '0.9.1',
+  globals = '0.16.3',
+  parallelly = '1.38.0',
+  future = '1.34.0',
+  future.apply = '1.11.2',
+  RcppEigen = '0.3.3.9.3',
+  RcppAnnoy = '0.0.19',
+  zoo = '1.8-12',
+  lmtest = '0.9-40',
+  fitdistrplus = '1.1-8',
+  caTools = '1.18.2',
+  gplots = '3.1.3',
+  ROCR = '1.0-11',
+  igraph = '2.0.3',
+  pbapply = '1.5-0',
+  commonmark = '1.9.0',
+  httpuv = '1.6.15',
+  sourcetools = '0.1.7-1',
+  shiny = '1.9.1',
+  miniUI = '0.1.1.1',
+  progressr = '0.14.0',
+  sitmo = '2.0.2',
+  dqrng = '0.4.1',
+  FNN = '1.1.3.2',
+  RcppProgress = '0.4.2',
+  uwot = '0.1.14',
+  cowplot = '1.1.1',
+  RcppTOML = '0.2.2',
+  rprojroot = '2.0.4',
+  here = '1.0.1',
+  reticulate = '1.40.0',
+  leiden = '0.4.3',
+  RANN = '2.6.1',
+  RcppArmadillo = '0.12.4.0.0',
+  sctransform = '0.3.4',
+  Rhdf5lib = '1.16.0',
+  xgboost = '1.7.8.1',
+  nidapFunctions = '0.7.8',
+  snow = '0.4-4',
+  BH = '1.81.0-1',
+  futile.options = '1.0.1',
+  futile.logger = '1.4.3',
+  base64enc = '0.1-3',
+  htmltools = '0.5.8.1',
+  rappdirs = '0.3.3',
+  jquerylib = '0.1.4',
+  tinytex = '0.44',
+  fs = '1.6.4',
+  sass = '0.4.6',
+  mime = '0.12',
+  magrittr = '2.0.3',
+  stringi = '1.8.4',
+  stringr = '1.5.1',
+  highr = '0.10',
+  knitr = '1.48',
+  fontawesome = '0.5.1',
+  rmarkdown = '2.28',
+  htmlwidgets = '1.6.4',
+  sys = '3.4.2',
+  askpass = '1.1',
+  openssl = '2.0.5',
+  curl = '6.4.0',
+  httr = '1.4.7',
+  timechange = '0.2.0',
+  lubridate = '1.8.0',
+  isoband = '0.2.7',
+  tibble = '3.2.1',
+  ggplot2 = '3.3.6',
+  patchwork = '1.2.0',
+  later = '1.3.2',
+  promises = '1.3.0',
+  crosstalk = '1.2.0',
+  purrr = '1.0.2',
+  tidyselect = '1.2.1',
+  dplyr = '1.1.4',
+  tidyr = '1.2.1',
+  plotly = '4.10.4',
+  plyr = '1.8.7',
+  clipr = '0.8.0',
+  prettyunits = '1.1.1',
+  progress = '1.2.2',
+  tzdb = '0.4.0',
+  vroom = '1.6.3',
+  readr = '2.1.2',
+  reshape2 = '1.4.4',
+  plogr = '0.2.0',
+  RSQLite = '2.3.9',
+  systemfonts = '1.2.3',
+  textshaping = '0.3.6',
+  ragg = '1.2.5',
+  dbplyr = '2.2.1',
+  rstudioapi = '0.14',
+  dtplyr = '1.3.1',
+  backports = '1.4.1',
+  broom = '1.0.1',
+  processx = '3.8.5',
+  callr = '3.7.3',
+  reprex = '2.0.2',
+  modelr = '0.1.9',
+  conflicted = '1.2.0',
+  rematch2 = '2.1.2',
+  gargle = '1.3.0',
+  rematch = '1.0.1',
+  cellranger = '1.1.0',
+  ids = '1.0.1',
+  googledrive = '2.0.0',
+  googlesheets4 = '1.0.1',
+  readxl = '1.4.1',
+  selectr = '0.4-2',
+  xml2 = '1.3.3',
+  rvest = '1.0.3',
+  forcats = '0.5.2',
+  haven = '2.5.1',
+  tidyverse = '1.3.2',
+  doParallel = '1.0.17',
+  MatrixGenerics = '1.6.0',
+  svglite = '2.1.0',
+  svMisc = '1.2.3',
+  xts = '0.12.2',
+  TTR = '0.24.3'
+)
+for (pkg in names(special_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = special_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version for ', pkg, ' failed, trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+EOFSPEC
+
+RUN R --vanilla --slave --file=/tmp/install_special.R
+
+# Install development dependencies
+RUN cat > /tmp/install_dev_dependencies.R << 'EOFDEV'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+dev_dependencies <- c('cffr', 'covr', 'goodpractice', 'here', 'lintr', 'pkgdown', 'rcmdcheck')
+
+for (pkg in dev_dependencies) {
+  tryCatch({
+    remotes::install_version(pkg, repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version failed for ', pkg, ', trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+EOFDEV
+
+RUN R --vanilla --slave --file=/tmp/install_dev_dependencies.R
+
+# Verify that all dependencies from DESCRIPTION are installed
+RUN cat > /tmp/check_description_deps.R << 'EOF'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+# Read the DESCRIPTION file
+desc_file <- "/opt/SCWorkflow/DESCRIPTION"
+if (!file.exists(desc_file)) {
+  stop("DESCRIPTION file not found at ", desc_file)
+}
+# Parse dependencies from DESCRIPTION
+desc <- read.dcf(desc_file)
+deps <- unique(c(
+  strsplit(desc[1, "Imports"], ",")[[1]],
+  strsplit(desc[1, "Suggests"], ",")[[1]],
+  strsplit(desc[1, "Depends"], ",")[[1]]
+))
+deps <- trimws(deps)
+# Check if each dependency is installed
+missing <- deps[!vapply(deps, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1))]
+if (length(missing) > 0) {
+  stop("The following dependencies are missing: ", paste(missing, collapse = ", "))
+} else {
+  message("All dependencies are installed.")
+}
+EOF
+
+RUN R --vanilla --slave --file=/tmp/check_description_deps.R
+
+COPY Dockerfile /