diff --git a/.github/workflows/Manual_Deployment_to_NIDAP.yml b/.github/workflows/Manual_Deployment_to_NIDAP.yml
new file mode 100644
index 0000000..2426e58
--- /dev/null
+++ b/.github/workflows/Manual_Deployment_to_NIDAP.yml
@@ -0,0 +1,105 @@
+name: Manual Deployment to NIDAP
+run-name: Manual Deployment to NIDAP by ${{ github.actor }} 
+
+on:
+  workflow_dispatch:
+    inputs:
+    
+      image_to_use:
+        required: true
+        default: "<Replace with your image>"
+        type: string
+
+      package_to_deploy:
+        required: true
+        type: string
+      
+      artifact_rid:
+        required: true
+        default: "<Replace with your artifact RID>"
+        type: string
+
+      token_to_use:
+        required: true
+        type: string
+      
+      
+jobs:
+  Adding_documentation_files_and_publish_page:
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ inputs.image_to_use }}
+      credentials:
+         username: ${{ github.actor }}
+         password: ${{ secrets.GITHUB_TOKEN }}
+         
+    steps:
+      - run: echo "Checking in ${{ inputs.image_to_use }}"
+      - uses: actions/checkout@v3
+        with:
+          token: ${{secrets.GITHUB_TOKEN}}
+          
+      - name: Continuous Deployment to NIDAP
+        id: nidap-cd
+        run: |
+          export current_wd="/__w/${GITHUB_REPOSITORY#*/}/${GITHUB_REPOSITORY#*/}"
+          cd $current_wd
+
+          export MY_GIT_TOKEN=${{ secrets.GITHUB_TOKEN }}
+          export MY_GIT_USERNAME=${{ github.actor }}
+          export MY_GIT_EMAIL=${{ github.event.pusher.email }}
+          
+          git config --global user.name "$MY_GIT_USERNAME"
+          git config --global user.email "$MY_GIT_EMAIL"
+          git config --global url."https://api:$MY_GIT_TOKEN@github.com/".insteadOf "https://github.com/"
+          git config --global url."https://ssh:$MY_GIT_TOKEN@github.com/".insteadOf "ssh://git@github.com/"
+          git config --global url."https://git:$MY_GIT_TOKEN@github.com/".insteadOf "git@github.com:"
+          
+          git config --global --add safe.directory "$current_wd"
+          
+          git clone https://github.com/${GITHUB_REPOSITORY}.git
+          
+          cd ${GITHUB_REPOSITORY#*/}
+
+          BRANCH_NAME="Conda_Package"
+
+          git checkout $BRANCH_NAME
+
+          echo "########## Git setup complete, moving to deployment... ##########"
+
+          conda install curl
+
+          current_pkg="${{ inputs.package_to_deploy }}"
+          
+          echo "Package to Upload: $current_pkg"
+
+          TOKEN="${{ inputs.token_to_use }}"
+          PACKAGE="$current_pkg"
+          PLATFORM="linux-64" # replace with the package platform (e.g. noarch, linux-64, osx-64)
+          response=$(curl \
+                    -H "Authorization: Bearer $TOKEN" \
+                    -H "Content-Type: application/octet-stream" \
+                    --data-binary "@$PACKAGE" \
+                    -XPUT "https://nidap.nih.gov/artifacts/api/repositories/${{ inputs.artifact_rid }}/contents/release/conda/$PLATFORM/$PACKAGE" \
+                    2>&1)
+
+
+          echo "#########################################################"
+
+          current_datetime="$(date +"%Y-%m-%d %H:%M:%S")"
+
+          # Check if the response contains an error message
+          if echo "$response" | grep -q "errorCode"; then
+            status=$(echo "$response" | grep -o '"errorName":"[^"]*' | awk -F'"' '{print $4}')
+            echo "Error message: $status"
+            echo "<br>Deployment Time: $current_datetime; Deployment Status: $status" >> README.md
+          else
+            status="Success"
+            echo "Update Success!"
+            echo "Package ${{ env.current_pkg }} is now on NIDAP."
+            echo "<br>Deployment Time: $current_datetime; Deployment Status: Success" >> README.md
+          fi
+
+          git commit -a -m "Deployment Performed on $current_datetime with Status: $status."
+
+          git push -f origin $BRANCH_NAME    
diff --git a/.github/workflows/gitflow-R-action.yml b/.github/workflows/gitflow-R-action.yml
index ac68e6a..ccecd82 100644
--- a/.github/workflows/gitflow-R-action.yml
+++ b/.github/workflows/gitflow-R-action.yml
@@ -1,9 +1,9 @@
 name: Gitflow Action for R Package Development
-run-name: ${{ github.actor }} now ${{ github.event_name }} to ${{ github.ref_name }}
+run-name: ${{ github.actor }} ${{ github.event_name }} to ${{ github.ref_name }}
 
 on:
   push:
-    branches: ['*', '!dev', '!main']
+    branches: ['*', '!dev', '!main', '!release_dev', '!Conda_Package', '!github_page']
     
   pull_request:
     types: ['opened', 'closed']
@@ -11,7 +11,13 @@ on:
 
 jobs:
   Activating_Parser:
-    uses: fnlcr-bids-sdsi/gitflow-R/.github/workflows/parser.yml@DSPWorkflow
+    uses: fnlcr-bids-sdsi/gitflow-R/.github/workflows/parser.yml@master
     with:
       image_to_use: ghcr.io/nidap-community/dsp_ci_cd:latest
-
+      package_name: "r-dspworkflow"
+      r_version: "4.1.3"
+      artifact_rid_production: "ri.artifacts.main.repository.20ce29a2-3803-4eae-b325-8fe367d47d1e"
+      artifact_rid_development: "ri.stemma.main.repository.2172e505-c98f-43d4-881a-47e170aadbe1"
+    secrets:
+      NIDAP_TOKEN_PRODUCTION: ${{ secrets.NIDAP_TOKEN_PRODUCTION }}
+      NIDAP_TOKEN_DEVELOPMENT: ${{ secrets.NIDAP_TOKEN_DEVELOPMENT }}
diff --git a/Conda_Recipe/meta.yaml b/Conda_Recipe/meta.yaml
new file mode 100644
index 0000000..11c3854
--- /dev/null
+++ b/Conda_Recipe/meta.yaml
@@ -0,0 +1,109 @@
+{% set version = '<CURRENT_VERSION>' %}
+
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-dspworkflow-test
+  version: {{ version|replace("-", "_") }}
+
+channels:
+  - conda-forge
+  - bioconda
+  - file:///local_channel
+
+source:
+
+  git_url: https://github.com/NIDAP-Community/DSPWorkflow/
+  git_tag: continuous_deployment
+
+build:
+  merge_build_host: True  # [win]
+  # If this is a new build for the same version, increment the build number.
+  number: 0
+  # no skip
+
+  # This is required to make R link correctly on Linux.
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+# Suggests: testthat (== 3.1.4)
+requirements:
+  build:
+    - {{ posix }}filesystem        # [win]
+    - {{ posix }}git
+    - {{ posix }}zip               # [win]
+
+  host:
+    - r-base =4.1.3=h2f963a2_5
+    - bioconductor-biobase =2.54.0=r41hc0cfd56_2
+    - bioconductor-biocgenerics =0.40.0=r41hdfd78af_0
+    - bioconductor-geomxtools =3.1.1=r41hdfd78af_0
+    - bioconductor-nanostringnctools =1.2.0
+    - bioconductor-spatialdecon =1.4.3
+    - bioconductor-complexheatmap =2.10.0=r41hdfd78af_0
+    - bioconductor-genomeinfodbdata =1.2.6
+    - r-cowplot =1.1.1=r41hc72bb7e_1
+    - r-dplyr =1.0.9=r41h7525677_0
+    - r-ggforce =0.3.4=r41h7525677_0
+    - r-ggplot2 =3.3.6=r41hc72bb7e_1
+    - r-gridextra =2.3=r41hc72bb7e_1004
+    - r-gtable =0.3.0=r41hc72bb7e_3
+    - r-knitr =1.40=r41hc72bb7e_1
+    - r-patchwork =1.1.2=r41hc72bb7e_1
+    - r-reshape2 =1.4.4=r41h7525677_2
+    - r-scales =1.2.1=r41hc72bb7e_1
+    - r-tibble =3.1.8=r41h06615bd_1
+    - r-tidyr =1.2.1=r41h7525677_1
+    - r-umap =0.2.9.0=r41h7525677_1
+    - r-rtsne =0.16=r41h37cf8d7_1
+    - r-magrittr =2.0.3=r41h06615bd_1
+    - r-rlang =1.1.0=r41h38f115c_0
+    - r-ggiraph=0.7.10=r41h03ef668_0
+    
+  run:
+    - r-base =4.1.3=h2f963a2_5
+    - bioconductor-biobase =2.54.0=r41hc0cfd56_2
+    - bioconductor-biocgenerics =0.40.0=r41hdfd78af_0
+    - bioconductor-geomxtools =3.1.1=r41hdfd78af_0
+    - bioconductor-nanostringnctools =1.2.0
+    - bioconductor-spatialdecon =1.4.3
+    - bioconductor-complexheatmap =2.10.0=r41hdfd78af_0
+    - bioconductor-genomeinfodbdata =1.2.6  
+    - r-cowplot =1.1.1=r41hc72bb7e_1
+    - r-dplyr =1.0.9=r41h7525677_0
+    - r-ggforce =0.3.4=r41h7525677_0
+    - r-ggplot2 =3.3.6=r41hc72bb7e_1
+    - r-gridextra =2.3=r41hc72bb7e_1004
+    - r-gtable =0.3.0=r41hc72bb7e_3
+    - r-knitr =1.40=r41hc72bb7e_1
+    - r-patchwork =1.1.2=r41hc72bb7e_1
+    - r-reshape2 =1.4.4=r41h7525677_2
+    - r-scales =1.2.1=r41hc72bb7e_1
+    - r-tibble =3.1.8=r41h06615bd_1
+    - r-tidyr =1.2.1=r41h7525677_1
+    - r-umap =0.2.9.0=r41h7525677_1
+    - r-rtsne =0.16=r41h37cf8d7_1
+    - r-magrittr =2.0.3=r41h06615bd_1
+    - r-rlang =1.1.0=r41h38f115c_0
+    - r-ggiraph=0.7.10=r41h03ef668_0
+
+test:
+  commands:
+    # You can put additional test commands to be run here.
+    - $R -e "library('DSPWorkflow')"           # [not win]
+    - "\"%R%\" -e \"library('DSPWorkflow')\""  # [win]
+
+about:
+  home: https://github.com/NIDAP-Community/DSPWorkflow
+  license: MIT
+  summary: A set of functions for analyzing RNA data from the spatial transcriptomics approach
+    Digital Spatial Profiling (Nanostring). The user provides read count data and annotations,
+    and the package outputs normalized differential expression of genes and further
+    visualizations and analysis based on user input. It can be run in a docker container
+    and in user-friendly web-based interactive notebooks (NIDAP, Palantir Foundry).
+  license_family: MIT
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT'
+    - LICENSE
diff --git a/Dockerfile/Conda_container/Building_R_environment/DESCRIPTION b/Dockerfile/Conda_container/Building_R_environment/DESCRIPTION
new file mode 100755
index 0000000..742b9cc
--- /dev/null
+++ b/Dockerfile/Conda_container/Building_R_environment/DESCRIPTION
@@ -0,0 +1,41 @@
+Type: project
+Description: Digital-Spatial-Profiling v3.1.1 environment for DSP package.
+Repository:
+    CRAN,
+    biocsoftv314,
+    biocsoftv315,
+    biocanadatav313,
+    biocexpdatav314,
+    biocworkflowv314
+Depends:
+    backports (== 1.4.1),
+    Biobase (== 2.54.0),
+    BiocGenerics (== 0.40.0),
+    cowplot (== 1.1.1),
+    dplyr (== 1.0.9),
+    GeomxTools (== 3.1.1),
+    ggforce (== 0.3.4),
+    ggplot2 (== 3.3.6),
+    ggiraph (== 0.8.3),
+    dbplyr (== 2.2.1),
+    gridExtra (== 2.3),
+    gtable (== 0.3.0),
+    knitr (== 1.40),
+    NanoStringNCTools (== 1.4.0),
+    patchwork (== 1.1.2),
+    reshape2 (== 1.4.4),
+    Rmpfr (== 0.8-9),
+    Rtsne (== 0.16),
+    scales (== 1.2.1),
+    stats (== 4.1.3),
+    SpatialDecon (== 1.4.3),
+    tibble (== 3.1.8),
+    tidyr (== 1.2.1),
+    tidyverse (== 1.3.2),
+    umap (== 0.2.9.0),
+    pheatmap (== 1.0.12),
+    stringr
+Remotes:
+    url::https://bioconductor.org/packages/3.15/workflows/src/contrib/GeoMxWorkflows_1.2.0.tar.gz,
+    git::https://github.com/Nanostring-Biostats/SpatialOmicsOverlay.git,
+    git::https://github.com/Nanostring-Biostats/GeomxTools.git
diff --git a/Dockerfile/Conda_container/Building_R_environment/Generate_Renv.R b/Dockerfile/Conda_container/Building_R_environment/Generate_Renv.R
new file mode 100755
index 0000000..1d15285
--- /dev/null
+++ b/Dockerfile/Conda_container/Building_R_environment/Generate_Renv.R
@@ -0,0 +1,44 @@
+# 9/13/2022 her2@nih.gov
+# Creating renv environment now
+
+#############################################################
+
+print("Loading repos...")
+repos <- c(CRAN = "https://cloud.r-project.org", 
+           biocsoftv314 = "https://bioconductor.org/packages/3.14/bioc/",
+           biocsoftv315 = "https://bioconductor.org/packages/3.15/bioc/",
+           biocanadatav313 = "https://bioconductor.org/packages/3.14/data/annotation/",
+           biocexpdatav314 = "https://bioconductor.org/packages/3.14/data/experiment/",
+           biocworkflowv314 = "https://bioconductor.org/packages/3.14/workflows/")
+options(repos = repos)
+print("Repos loaded.")
+
+###############################################################
+
+print("Setting up plain R environment now...")
+
+if(!file.exists("DESCRIPTION")){
+  
+  print("No existing DESCRIPTION file in current working directory:")
+  print(getwd())
+  print("Exiting Environment setup now.")
+  
+  auto.snapshot <- getOption("renv.config.auto.snapshot")
+  options(renv.config.auto.snapshot = TRUE)
+  break
+  
+}else{
+  
+  print("Installing Packages from DESCRIPTION now...")
+  
+  renv::install()
+  
+  print("Packages installed.")
+  
+
+  auto.snapshot <- getOption("renv.config.auto.snapshot")
+  options(renv.config.auto.snapshot = TRUE)
+  
+}
+
+
diff --git a/Dockerfile/Conda_container/Building_R_environment/Initiate_Renv.R b/Dockerfile/Conda_container/Building_R_environment/Initiate_Renv.R
new file mode 100755
index 0000000..917d480
--- /dev/null
+++ b/Dockerfile/Conda_container/Building_R_environment/Initiate_Renv.R
@@ -0,0 +1,18 @@
+# 9/13/2022 her2@nih.gov
+# Creating renv environment now
+
+# initiate <- FALSE
+if (initiate){
+  
+  auto.snapshot <- getOption("renv.config.auto.snapshot")
+  options(renv.config.auto.snapshot = FALSE)
+  
+  renv::settings$snapshot.type("implicit")
+  renv::init(bare = TRUE)
+  print("Environment Initiated")
+  
+}else{
+  
+  print("Environment Not Initiated")
+  
+}
\ No newline at end of file
diff --git a/Dockerfile/Conda_container/Building_R_environment/Load_packages.R b/Dockerfile/Conda_container/Building_R_environment/Load_packages.R
new file mode 100644
index 0000000..5911850
--- /dev/null
+++ b/Dockerfile/Conda_container/Building_R_environment/Load_packages.R
@@ -0,0 +1,17 @@
+print("Loading and recording sessionInfo now...")
+
+# Load packages
+list_of_package <- scan("package_list.txt", what="", sep="\n")
+
+for (packages in list_of_package){
+  lapply(packages,
+         function(x) suppressMessages(library(x,
+                                              character.only = TRUE,
+                                              quietly=TRUE,
+                                              warn.conflicts = FALSE)))
+}
+
+
+sessionInfoName <- "sessionInfo.txt"
+writeLines(capture.output(sessionInfo()), sessionInfoName)
+print("SessionInfo printed.")
diff --git a/Dockerfile/Conda_container/Building_R_environment/package_list.txt b/Dockerfile/Conda_container/Building_R_environment/package_list.txt
new file mode 100755
index 0000000..61514f3
--- /dev/null
+++ b/Dockerfile/Conda_container/Building_R_environment/package_list.txt
@@ -0,0 +1,6 @@
+GeomxTools
+NanoStringNCTools
+SpatialDecon
+tidyverse
+pheatmap
+stringr
\ No newline at end of file
diff --git a/Dockerfile/Conda_container/Dockerfile b/Dockerfile/Conda_container/Dockerfile
index 4c73272..2bb219d 100755
--- a/Dockerfile/Conda_container/Dockerfile
+++ b/Dockerfile/Conda_container/Dockerfile
@@ -26,7 +26,7 @@ RUN apt-get update && \
     add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0" && \
     add-apt-repository --enable-source --yes "ppa:c2d4u.team/c2d4u4.0+"
 
-## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
+# ## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
 RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
   locale-gen en_US.utf8 && \
 	/usr/sbin/update-locale LANG=en_US.UTF-8
@@ -34,10 +34,10 @@ RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
 ENV LC_ALL en_US.UTF-8
 ENV LANG en_US.UTF-8
 
-## Use Debian unstable via pinning -- new style via APT::Default-Release
-#RUN echo "deb http://http.debian.net/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list \
-#        && echo 'APT::Default-Release "testing";' > /etc/apt/apt.conf.d/default
-#
+# ## Use Debian unstable via pinning -- new style via APT::Default-Release
+# #RUN echo "deb http://http.debian.net/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list \
+# #        && echo 'APT::Default-Release "testing";' > /etc/apt/apt.conf.d/default
+# #
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -77,27 +77,30 @@ RUN apt-get update && \
 
 RUN apt-get -y update && apt-get -y install git
 
-# add the signing key (by Michael Rutter) for these repos
-# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
-# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
+# # add the signing key (by Michael Rutter) for these repos
+# # To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
+# # Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
 
-# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
+# # add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
 
 # ENV R_BASE_VERSION=4.1.3
 
 # RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc && \
 #    add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" && \
 #    add-apt-repository ppa:c2d4u.team/c2d4u4.0+ && \
-#    apt update &&
-#	  apt-get install -y --no-install-recommends \
-#	    r-cran-rjava \
-#      r-base-core=${R_BASE_VERSION}-* \
-#		  r-base-dev=${R_BASE_VERSION}-*
-#
+#    apt update && \
+#    apt-get install -y --no-install-recommends \
+#     r-cran-rjava \
+#     r-base-core=${R_BASE_VERSION}-* \
+# 	  r-base-dev=${R_BASE_VERSION}-*
+
 # RUN R -e 'install.packages("devtools")'
 # RUN R -e 'install.packages("renv")'
 # RUN R -e 'install.packages("lintr")'
 
+# RUN mkdir /renv_cache
+# ENV RENV_PATHS_CACHE="/renv_cache"
+
 # COPY Building_R_environment/* .
 
 # RUN R -e 'initiate=TRUE; source("Initiate_Renv.R"); source("Generate_Renv.R")'
@@ -107,12 +110,14 @@ ENV PATH="/root/miniconda3/bin:${PATH}"
 ARG PATH="/root/miniconda3/bin:${PATH}"
 
 RUN wget \
-    https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh \
-    && mkdir /root/.conda \
-    && bash Miniconda3-py37_4.8.2-Linux-x86_64.sh  -b \
-    && rm -f Miniconda3-py37_4.8.2-Linux-x86_64.sh
+    https://repo.anaconda.com/miniconda/Miniconda3-py38_22.11.1-1-Linux-x86_64.sh \
+#    && mkdir /root/.conda \
+    && bash Miniconda3-py38_22.11.1-1-Linux-x86_64.sh  -b \
+    && rm -f Miniconda3-py38_22.11.1-1-Linux-x86_64.sh
 
 RUN conda --version
+RUN conda install -n base conda-libmamba-solver \
+    && conda config --set solver libmamba
 
 RUN conda config --append channels defaults
 RUN conda config --append channels anaconda
@@ -127,36 +132,42 @@ RUN conda init bash
 
 ENV PATH /opt/conda/envs/env/bin:$PATH
 
-### For .yml method
-COPY environment.yml .
-RUN mamba env update -f environment.yml
-
-
-SHELL ["/bin/bash", "-c"]
-
-RUN echo "source activate DSPWorkflow_NIDAP" >> ~/.bashrc
+#SHELL ["/bin/bash", "-c"]
 
 RUN chmod -R ugo+rwx /opt
 RUN chmod -R ugo+rwx /tmp
 RUN echo "TMPDIR=/tmp" > /root/.Renviron
 
-RUN mkdir /tmp/local_conda_channel
-RUN mkdir /tmp/local_conda_channel/linux-64
+RUN mkdir /local_channel
+RUN mkdir /local_channel/linux-64
 RUN conda install conda-build
 
-COPY bioconductor-nanostringnctools-1.4.0-r41hdfd78af_0.tar.bz2 /tmp/local_conda_channel/linux-64
-COPY bioconductor-spatialdecon-1.4.3-r41hdfd78af_0.tar.bz2 /tmp/local_conda_channel/linux-64
-COPY bioconductor-geomxtools-3.1.1-r41hdfd78af_0.tar.bz2 /tmp/local_conda_channel/linux-64
-COPY bioconductor-geomxtools-3.1.1-r41hdfd78af_0.tar.bz2 /tmp/local_conda_channel/linux-64
-COPY bioconductor-nanostringnctools-1.2.0-r41hdfd78af_0.tar.bz2 /tmp/local_conda_channel/linux-64
+COPY bioconductor-nanostringnctools-1.4.0-r41hdfd78af_0.tar.bz2 /local_channel/linux-64
+COPY bioconductor-spatialdecon-1.4.3-r41hdfd78af_0.tar.bz2 /local_channel/linux-64
+COPY bioconductor-geomxtools-3.1.1-r41hdfd78af_0.tar.bz2 /local_channel/linux-64
+COPY bioconductor-nanostringnctools-1.2.0-r41hdfd78af_0.tar.bz2 /local_channel/linux-64
+
+RUN conda index /local_channel/
+
+RUN conda config --add channels file:///local_channel/
+
+### For .yml method
+COPY environment.yml .
+RUN mamba env update -f environment.yml
+
+RUN echo "source activate DSPWorkflow_NIDAP" >> ~/.bashrc
 
-RUN conda index /tmp/local_conda_channel/
+ENV PATH="/root/miniconda3/envs/DSPWorkflow_NIDAP/bin:$PATH"
 
-RUN conda config --add channels file:///tmp/local_conda_channel/
+# Create target directory
+RUN mkdir -p /renv/library/R-4.1/x86_64-pc-linux-gnu
 
-RUN mamba install --prefix ~/miniconda3/envs/DSPWorkflow_NIDAP -c file:///tmp/local_conda_channel/ bioconductor-geomxtools==3.1.1 bioconductor-spatialdecon==1.4.3
-# RUN mamba install --prefix ~/miniconda3/envs/DSPWorkflow_NIDAP -c file:///tmp/local_conda_channel/ bioconductor-nanostringnctools==1.4.0
+# Create symbolic links
+RUN for d in /root/miniconda3/envs/DSPWorkflow_NIDAP/lib/R/library/*; do \
+   if [ -d "$d" ]; then \
+       ln -s "$d" "/renv/library/R-4.1/x86_64-pc-linux-gnu/$(basename $d)"; \
+   fi \
+done
 
-COPY start_conda.sh .
+CMD ["bash"]
 
-CMD ["start_conda.sh"]
diff --git a/Dockerfile/Conda_container/environment.yml b/Dockerfile/Conda_container/environment.yml
index bd9510a..5633ab7 100644
--- a/Dockerfile/Conda_container/environment.yml
+++ b/Dockerfile/Conda_container/environment.yml
@@ -1,16 +1,19 @@
 channels:
 - bioconda
 - conda-forge
-- defaults
+- file:///local_channel
 dependencies:
 - r-base==4.1.3
 - r-backports==1.4.1 
 - bioconductor-biobase==2.54.0 
 - bioconductor-biocgenerics==0.40.0 
-- bioconductor-nanostringnctools=1.2.0
+- bioconductor-nanostringnctools=1.2.0 
+- bioconductor-geomxtools==3.1.1 
+- bioconductor-complexheatmap==2.10.0 
+- bioconductor-spatialdecon==1.4.3 
 - r-tidyverse==1.3.2 
 - r-cowplot==1.1.1 
-- r-dplyr==1.1.0 
+- r-dplyr==1.0.9 
 - r-ggforce==0.3.4 
 - r-ggplot2==3.3.6 
 - r-ggiraph==0.8.3
@@ -25,9 +28,12 @@ dependencies:
 - r-tibble==3.1.8 
 - r-tidyr==1.2.1 
 - r-umap==0.2.9.0 
-- r-pheatmap==1.0.12 
+- r-pheatmap==1.0.12
+- r-xlsx
 - r-stringr
 - r-devtools
 - r-lintr
 - r-renv
+- r-jsonlite
+- r-pkgdown
 name: DSPWorkflow_NIDAP
diff --git a/Dockerfile/Plain_R_container/Building_R_environment/DESCRIPTION b/Dockerfile/Plain_R_container/Building_R_environment/DESCRIPTION
index 742b9cc..e32227b 100755
--- a/Dockerfile/Plain_R_container/Building_R_environment/DESCRIPTION
+++ b/Dockerfile/Plain_R_container/Building_R_environment/DESCRIPTION
@@ -34,7 +34,10 @@ Depends:
     tidyverse (== 1.3.2),
     umap (== 0.2.9.0),
     pheatmap (== 1.0.12),
-    stringr
+    stringr,
+    complexheatmap (>=2.5.2),
+    xlsx,
+    jsonlite,
 Remotes:
     url::https://bioconductor.org/packages/3.15/workflows/src/contrib/GeoMxWorkflows_1.2.0.tar.gz,
     git::https://github.com/Nanostring-Biostats/SpatialOmicsOverlay.git,