diff --git a/.github/ISSUE_TEMPLATE/create-a-semantic-version-release.md b/.github/ISSUE_TEMPLATE/create-a-semantic-version-release.md
index bee31cedc..11f5f56e5 100644
--- a/.github/ISSUE_TEMPLATE/create-a-semantic-version-release.md
+++ b/.github/ISSUE_TEMPLATE/create-a-semantic-version-release.md
@@ -23,5 +23,5 @@ If issues must be resolved before creating a release, mark them as blockers in Z
   - Are there any _major_ shifts in project dependencies?
     For example, is there a package that was used throughout Docker environments that has been replaced?
   - Have there been any changes in repo file organization?
-- [ Create a release on GitHub ](https://github.com/AlexsLemonade/OpenScPCA-analysis/releases/new)
+- [ ] [Create a release on GitHub](https://github.com/AlexsLemonade/OpenScPCA-analysis/releases/new)
   - populate the contents with the release notes added to the changelog.
diff --git a/.github/workflows/build-push-docker-module.yml b/.github/workflows/build-push-docker-module.yml
index 305aa0d5d..07c3528ed 100644
--- a/.github/workflows/build-push-docker-module.yml
+++ b/.github/workflows/build-push-docker-module.yml
@@ -20,7 +20,7 @@ permissions:
 jobs:
   build-push:
     name: Build and Push Docker Image
-    if: inputs.push-ecr && github.repository_owner == 'AlexsLemonade'
+    if: github.repository_owner == 'AlexsLemonade'
     environment: prod
     runs-on: openscpca-22.04-big-disk
 
@@ -80,7 +80,7 @@ jobs:
         env:
           DOCKER_BUILD_SUMMARY: false
         with:
-          push: true
+          push: ${{ inputs.push-ecr }}
           context: "{{defaultContext}}:analyses/${{ inputs.module }}"
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/docker_all-modules.yml b/.github/workflows/docker_all-modules.yml
index 1e82c4a4a..ff7f53fab 100644
--- a/.github/workflows/docker_all-modules.yml
+++ b/.github/workflows/docker_all-modules.yml
@@ -69,7 +69,7 @@ jobs:
         if: contains(needs.*.result, 'failure')
         uses: peter-evans/create-issue-from-file@v5
         with:
-          title: Analysis module failing in CI
+          title: Docker image build failing in CI
           content-filepath: |
             .github/cron-issue-templates/all-docker-issue-template.md
           labels: |
diff --git a/.github/workflows/docker_celltype-glioblastoma.yml b/.github/workflows/docker_cell-type-glioblastoma.yml
similarity index 66%
rename from .github/workflows/docker_celltype-glioblastoma.yml
rename to .github/workflows/docker_cell-type-glioblastoma.yml
index 77f5421f1..ea4179ffa 100644
--- a/.github/workflows/docker_celltype-glioblastoma.yml
+++ b/.github/workflows/docker_cell-type-glioblastoma.yml
@@ -1,11 +1,11 @@
-# This is a workflow to build the docker image for the celltype-glioblastoma module
+# This is a workflow to build the docker image for the cell-type-glioblastoma module
 #
 # Docker modules are run on pull requests when code for files that affect the Docker image have changed.
 # If other files are used during the Docker build, they should be added to `paths`
 #
 # At module initialization, this workflow is inactive, and needs to be activated manually
 
-name: Build docker image for celltype-glioblastoma
+name: Build docker image for cell-type-glioblastoma
 
 concurrency:
   # only one run per branch at a time
@@ -17,18 +17,18 @@ on:
   #   branches:
   #     - main
   #   paths:
-  #     - "analyses/celltype-glioblastoma/Dockerfile"
-  #     - "analyses/celltype-glioblastoma/.dockerignore"
-  #     - "analyses/celltype-glioblastoma/renv.lock"
-  #     - "analyses/celltype-glioblastoma/conda-lock.yml"
+  #     - "analyses/cell-type-glioblastoma/Dockerfile"
+  #     - "analyses/cell-type-glioblastoma/.dockerignore"
+  #     - "analyses/cell-type-glioblastoma/renv.lock"
+  #     - "analyses/cell-type-glioblastoma/conda-lock.yml"
   # push:
   #   branches:
   #     - main
   #   paths:
-  #     - "analyses/celltype-glioblastoma/Dockerfile"
-  #     - "analyses/celltype-glioblastoma/.dockerignore"
-  #     - "analyses/celltype-glioblastoma/renv.lock"
-  #     - "analyses/celltype-glioblastoma/conda-lock.yml"
+  #     - "analyses/cell-type-glioblastoma/Dockerfile"
+  #     - "analyses/cell-type-glioblastoma/.dockerignore"
+  #     - "analyses/cell-type-glioblastoma/renv.lock"
+  #     - "analyses/cell-type-glioblastoma/conda-lock.yml"
   workflow_dispatch:
     inputs:
       push-ecr:
@@ -49,7 +49,7 @@ jobs:
       - name: Build image
         uses: docker/build-push-action@v5
         with:
-          context: "{{defaultContext}}:analyses/celltype-glioblastoma"
+          context: "{{defaultContext}}:analyses/cell-type-glioblastoma"
           push: false
           cache-from: type=gha
           cache-to: type=gha,mode=max
@@ -59,5 +59,5 @@ jobs:
     if: github.repository_owner == 'AlexsLemonade' && (github.event_name == 'push' || inputs.push-ecr)
     uses: ./.github/workflows/build-push-docker-module.yml
     with:
-      module: "celltype-glioblastoma"
+      module: "cell-type-glioblastoma"
       push-ecr: true
diff --git a/.github/workflows/run_celltype-glioblastoma.yml b/.github/workflows/run_cell-type-glioblastoma.yml
similarity index 82%
rename from .github/workflows/run_celltype-glioblastoma.yml
rename to .github/workflows/run_cell-type-glioblastoma.yml
index 3bffc5f93..b48d066fe 100644
--- a/.github/workflows/run_celltype-glioblastoma.yml
+++ b/.github/workflows/run_cell-type-glioblastoma.yml
@@ -1,4 +1,4 @@
-# This is a workflow to run the celltype-glioblastoma module
+# This is a workflow to run the cell-type-glioblastoma module
 #
 # Analysis modules are run based on three triggers:
 # - Manual trigger
@@ -7,9 +7,9 @@
 #
 # At initialization, only the manual trigger is active
 
-name: Run celltype-glioblastoma analysis module
+name: Run cell-type-glioblastoma analysis module
 env:
-  MODULE_PATH: analyses/celltype-glioblastoma
+  MODULE_PATH: analyses/cell-type-glioblastoma
   AWS_DEFAULT_REGION: us-east-2
 
 concurrency:
@@ -24,9 +24,9 @@ on:
   #   branches:
   #     - main
   #   paths:
-  #     - analyses/celltype-glioblastoma/**
-  #     - "!analyses/celltype-glioblastoma/Dockerfile"
-  #     - "!analyses/celltype-glioblastoma/.dockerignore"
+  #     - analyses/cell-type-glioblastoma/**
+  #     - "!analyses/cell-type-glioblastoma/Dockerfile"
+  #     - "!analyses/cell-type-glioblastoma/.dockerignore"
   #     - .github/workflows/run_celltype-glioblastoma.yml
 
 jobs:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7630f835b..af6e3e121 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,34 @@ Add new release notes in reverse numerical order (newest first) below this comme
 You may want to add temporary notes here for tracking as features are added, before a new release is ready.
 -->
 
+## v0.2.0
+
+This release adds the first set of community-contributed analyses to the repository.
+These modules are focused on cell type identification and annotation for specific ScPCA datasets.
+Note that many of these modules are still in development at this stage and may not be fully functional.
+
+- `cell-type-dsrct`
+- `cell-type-ETP-ALL-03`
+- `cell-type-glioblastoma`
+- `cell-type-nonETP-ALL-03`
+- `cell-type-wilms-tumor-06`
+- `cell-type-wilms-tumor-14`
+
+
+This release also adds the following new modules developed by the Data Lab:
+
+- `cell-type-consensus`: a module for exploring consensus cell types across multiple annotation methods
+- `hello-clusters`: a demonstration module for clustering analysis using the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA)
+- `seurat-conversion`: a module for converting `SingleCellExperiment` objects to Seurat objects, also using the `rOpenScPCA` package
+
+Other updates in this release include:
+
+- a new `sync-results.py` script to simplify uploading (and downloading) analysis results from an analysis module to a user's S3 bucket
+- changes from `miniconda` to `miniforge` for conda usage throughout the project
+
+While not part of this repository, we do want to also note that we have created the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA), which will house utility functions commonly used by analysis modules here.
+The goal is to centralize common functions used across analysis modules to make it easier to share code and maintain consistency across modules.
+
 
 ## v0.1.0
 
@@ -17,7 +45,7 @@ The repository at this stage should be generally complete with respect to infras
 
 With respect to infrastructure, the repository contains the following components:
 
-- detailed documentation in the `docs` directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io) 
+- detailed documentation in the `docs` directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io)
 - a `create-analysis-module.py` script for setting up new analysis modules
 - `download-data.py` and `download-results.py` scripts to download data and results from the OpenScPCA project
 - template notebooks, scripts, environment files, and Docker images for analysis modules
diff --git a/analyses/celltype-glioblastoma/.dockerignore b/analyses/cell-type-glioblastoma/.dockerignore
similarity index 100%
rename from analyses/celltype-glioblastoma/.dockerignore
rename to analyses/cell-type-glioblastoma/.dockerignore
diff --git a/analyses/celltype-glioblastoma/.gitignore b/analyses/cell-type-glioblastoma/.gitignore
similarity index 100%
rename from analyses/celltype-glioblastoma/.gitignore
rename to analyses/cell-type-glioblastoma/.gitignore
diff --git a/analyses/celltype-glioblastoma/Dockerfile b/analyses/cell-type-glioblastoma/Dockerfile
similarity index 100%
rename from analyses/celltype-glioblastoma/Dockerfile
rename to analyses/cell-type-glioblastoma/Dockerfile
diff --git a/analyses/celltype-glioblastoma/README.md b/analyses/cell-type-glioblastoma/README.md
similarity index 100%
rename from analyses/celltype-glioblastoma/README.md
rename to analyses/cell-type-glioblastoma/README.md
diff --git a/analyses/celltype-glioblastoma/environment.yml b/analyses/cell-type-glioblastoma/environment.yml
similarity index 85%
rename from analyses/celltype-glioblastoma/environment.yml
rename to analyses/cell-type-glioblastoma/environment.yml
index 5e8844ce9..6c683643a 100644
--- a/analyses/celltype-glioblastoma/environment.yml
+++ b/analyses/cell-type-glioblastoma/environment.yml
@@ -1,4 +1,4 @@
-name: "openscpca-celltype-glioblastoma"
+name: "openscpca-cell-type-glioblastoma"
 channels:
   - conda-forge
   - bioconda
diff --git a/analyses/cell-type-glioblastoma/notebook-template.ipynb b/analyses/cell-type-glioblastoma/notebook-template.ipynb
new file mode 100644
index 000000000..b0e85e1f4
--- /dev/null
+++ b/analyses/cell-type-glioblastoma/notebook-template.ipynb
@@ -0,0 +1,310 @@
+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "id": "5ecf8d71-c970-49ad-a908-fb94f43835e9",
+      "metadata": {},
+      "source": [
+        "# cell-type-glioblastoma Analysis\n",
+        "\n",
+        "_Author Name_\n",
+        "\n",
+        "_Date_\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "abd58442",
+      "metadata": {},
+      "source": [
+        "## Introduction\n",
+        "\n",
+        "This a template for an analysis notebook using Jupyter.\n",
+        "\n",
+        "It is a good idea to start with a brief introduction to the analysis, including the purpose of the analysis, the data used, and the methods applied.\n",
+        "Replace this text with your own introduction, and be sure to update the _Title_, _Author Name_, and _Date_ at the top of the document.\n",
+        "\n",
+        "Don't forget to rename this file as well!\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "f7e42626",
+      "metadata": {},
+      "source": [
+        "## Setup\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "b3d030d5",
+      "metadata": {},
+      "source": [
+        "### Load modules\n",
+        "\n",
+        "Load required Python modules in the following cell.\n",
+        "We have included the standard `pathlib` module and the `session_info` module that we will be using at the bottom of this notebook to record the versions of the modules used in this analysis.\n",
+        "\n",
+        "Do not install modules here; only load them with `import` statements.\n",
+        "Avoid renaming modules with `as` statements, unless you are performing a standard renaming (e.g., `import pandas as pd`).\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 1,
+      "id": "922376d5-331e-4966-910c-1f5540fdc230",
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "# import required modules\n",
+        "import pathlib\n",
+        "\n",
+        "import session_info"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "7f5a9354",
+      "metadata": {},
+      "source": [
+        "### Paths\n",
+        "\n",
+        "Setting paths to directories and files for input and output at the start of a notebook can be helpful for organization and reproducibility.\n",
+        "You may not know all of the paths you need when you start a notebook, but once you do, keeping them all in one place is helpful, both for yourself in the future and for other users of the notebook.\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "86d81532",
+      "metadata": {},
+      "source": [
+        "#### Base directories\n",
+        "\n",
+        "In the cell below, we include some common directories that you might need in your analysis.\n",
+        "We find the repository root by looking for a (hidden) `.git` directory somewhere in the file path that contains this file, then set the data directory and module directories relative to that.\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 2,
+      "id": "d124fed2",
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "# Find the repository root directory\n",
+        "repo_root = pathlib.Path.cwd()\n",
+        "while not (repo_root / \".git\").is_dir():  # search for the .git directory\n",
+        "    repo_root = repo_root.parent\n",
+        "    if repo_root == \"/\":\n",
+        "        raise FileNotFoundError(\"Could not find the repository root directory\")\n",
+        "\n",
+        "# set module path (using pathlib)\n",
+        "module_root = repo_root / \"analyses\" / \"cell-type-glioblastoma\"\n",
+        "\n",
+        "# set current data directory\n",
+        "data_dir = repo_root / \"data\" / \"current\"\n",
+        "\n",
+        "# set results and plots directories (using the analysis project file to find root)\n",
+        "results_dir = module_root / \"results\"\n",
+        "plots_dir = module_root / \"plots\""
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "b40fb5e9",
+      "metadata": {},
+      "source": [
+        "#### Input and output files\n",
+        "\n",
+        "Set paths to input and output directories and files in the cell below.\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 3,
+      "id": "49c1e1c1",
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "# Input files\n",
+        "\n",
+        "# Output files\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "f1fbe4b6",
+      "metadata": {
+        "jp-MarkdownHeadingCollapsed": true
+      },
+      "source": [
+        "## Analysis content\n",
+        "\n",
+        "Organize the remainder of your content into sections and subsections as appropriate for your analysis.\n",
+        "\n",
+        "Add new Code and Markdown cells as needed using the Jupyter interface or your favorite keyboard shortcuts.\n",
+        "For example, you can use **Alt+Enter** on Windows or Linux or **Opt+Return** on a Mac to execute the current cell and insert a new one below.\n",
+        "\n",
+        "Be sure to comment your code and explain your steps as you go.\n",
+        "\n",
+        "It is usually a good idea to rerun the entire notebook before sharing any output, to ensure that the notebook and output files are fully up to date.\n",
+        "You can do this in the Jupyter Lab or Notebook interface by clicking on the _Kernel_ menu and choosing _Restart Kernel and Run All Cells..._\n"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "id": "d1b4d0c9",
+      "metadata": {},
+      "source": [
+        "## Session Info\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 4,
+      "id": "eb4d84a4",
+      "metadata": {},
+      "outputs": [
+        {
+          "data": {
+            "text/html": [
+              "<details>\n",
+              "<summary>Click to view session information</summary>\n",
+              "<pre>\n",
+              "-----\n",
+              "session_info        1.0.0\n",
+              "-----\n",
+              "</pre>\n",
+              "<details>\n",
+              "<summary>Click to view modules imported as dependencies</summary>\n",
+              "<pre>\n",
+              "CoreFoundation              NA\n",
+              "Foundation                  NA\n",
+              "PyObjCTools                 NA\n",
+              "anyio                       NA\n",
+              "appnope                     0.1.4\n",
+              "arrow                       1.3.0\n",
+              "asttokens                   NA\n",
+              "attr                        23.2.0\n",
+              "attrs                       23.2.0\n",
+              "babel                       2.14.0\n",
+              "brotli                      1.1.0\n",
+              "certifi                     2024.02.02\n",
+              "charset_normalizer          3.3.2\n",
+              "colorama                    0.4.6\n",
+              "comm                        0.2.2\n",
+              "cython_runtime              NA\n",
+              "dateutil                    2.8.2\n",
+              "debugpy                     1.8.1\n",
+              "decorator                   5.1.1\n",
+              "executing                   2.0.1\n",
+              "fastjsonschema              NA\n",
+              "fqdn                        NA\n",
+              "idna                        3.6\n",
+              "ipykernel                   6.29.3\n",
+              "isoduration                 NA\n",
+              "jedi                        0.19.1\n",
+              "jinja2                      3.1.3\n",
+              "json5                       0.9.24\n",
+              "jsonpointer                 2.4\n",
+              "jsonschema                  4.21.1\n",
+              "jsonschema_specifications   NA\n",
+              "jupyter_events              0.10.0\n",
+              "jupyter_server              2.13.0\n",
+              "jupyterlab_server           2.25.4\n",
+              "markupsafe                  2.1.5\n",
+              "nbformat                    5.10.3\n",
+              "objc                        10.2\n",
+              "overrides                   NA\n",
+              "packaging                   24.0\n",
+              "parso                       0.8.3\n",
+              "pexpect                     4.9.0\n",
+              "pickleshare                 0.7.5\n",
+              "platformdirs                4.2.0\n",
+              "prometheus_client           NA\n",
+              "prompt_toolkit              3.0.38\n",
+              "psutil                      5.9.8\n",
+              "ptyprocess                  0.7.0\n",
+              "pure_eval                   0.2.2\n",
+              "pydev_ipython               NA\n",
+              "pydevconsole                NA\n",
+              "pydevd                      2.9.5\n",
+              "pydevd_file_utils           NA\n",
+              "pydevd_plugins              NA\n",
+              "pydevd_tracing              NA\n",
+              "pygments                    2.17.2\n",
+              "pythonjsonlogger            NA\n",
+              "referencing                 NA\n",
+              "requests                    2.31.0\n",
+              "rfc3339_validator           0.1.4\n",
+              "rfc3986_validator           0.1.1\n",
+              "rpds                        NA\n",
+              "ruamel                      NA\n",
+              "send2trash                  NA\n",
+              "six                         1.16.0\n",
+              "sniffio                     1.3.1\n",
+              "socks                       1.7.1\n",
+              "stack_data                  0.6.2\n",
+              "tornado                     6.4\n",
+              "traitlets                   5.14.2\n",
+              "uri_template                NA\n",
+              "urllib3                     1.26.18\n",
+              "wcwidth                     0.2.13\n",
+              "webcolors                   1.13\n",
+              "websocket                   1.7.0\n",
+              "yaml                        6.0.1\n",
+              "zmq                         25.1.2\n",
+              "</pre>\n",
+              "</details> <!-- seems like this ends pre, so might as well be explicit -->\n",
+              "<pre>\n",
+              "-----\n",
+              "IPython             8.17.2\n",
+              "jupyter_client      8.6.1\n",
+              "jupyter_core        5.7.2\n",
+              "jupyterlab          4.1.5\n",
+              "notebook            7.1.2\n",
+              "-----\n",
+              "Python 3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:49:36) [Clang 16.0.6 ]\n",
+              "macOS-14.3.1-arm64-arm-64bit\n",
+              "-----\n",
+              "Session information updated at 2024-03-20 18:04\n",
+              "</pre>\n",
+              "</details>"
+            ],
+            "text/plain": [
+              "<IPython.core.display.HTML object>"
+            ]
+          },
+          "execution_count": 4,
+          "metadata": {},
+          "output_type": "execute_result"
+        }
+      ],
+      "source": [
+        "# record the versions of the modules used in this analysis and other environment information\n",
+        "session_info.show()"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3 (ipykernel)",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.11.8"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 5
+}
diff --git a/analyses/celltype-glioblastoma/plots/.gitkeep b/analyses/cell-type-glioblastoma/plots/.gitkeep
similarity index 100%
rename from analyses/celltype-glioblastoma/plots/.gitkeep
rename to analyses/cell-type-glioblastoma/plots/.gitkeep
diff --git a/analyses/celltype-glioblastoma/results/README.md b/analyses/cell-type-glioblastoma/results/README.md
similarity index 100%
rename from analyses/celltype-glioblastoma/results/README.md
rename to analyses/cell-type-glioblastoma/results/README.md
diff --git a/analyses/celltype-glioblastoma/scratch/.gitkeep b/analyses/cell-type-glioblastoma/scratch/.gitkeep
similarity index 100%
rename from analyses/celltype-glioblastoma/scratch/.gitkeep
rename to analyses/cell-type-glioblastoma/scratch/.gitkeep
diff --git a/analyses/celltype-glioblastoma/script-template.py b/analyses/cell-type-glioblastoma/script-template.py
similarity index 95%
rename from analyses/celltype-glioblastoma/script-template.py
rename to analyses/cell-type-glioblastoma/script-template.py
index 9365e3cde..8b7cd680a 100644
--- a/analyses/celltype-glioblastoma/script-template.py
+++ b/analyses/cell-type-glioblastoma/script-template.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# celltype-glioblastoma Analysis Script
+# cell-type-glioblastoma Analysis Script
 # Author Name
 # Date
 #
@@ -55,7 +55,7 @@ def find_git_root():
 repo_root = find_git_root()
 
 # set module path (using pathlib)
-module_root = repo_root / "analyses" / "celltype-glioblastoma"
+module_root = repo_root / "analyses" / "cell-type-glioblastoma"
 
 # set current data directory
 data_dir = repo_root / "data" / "current"
diff --git a/analyses/celltype-glioblastoma/scripts/.gitkeep b/analyses/cell-type-glioblastoma/scripts/.gitkeep
similarity index 100%
rename from analyses/celltype-glioblastoma/scripts/.gitkeep
rename to analyses/cell-type-glioblastoma/scripts/.gitkeep
diff --git a/analyses/celltype-glioblastoma/notebook-template.ipynb b/analyses/celltype-glioblastoma/notebook-template.ipynb
deleted file mode 100644
index cb37c0446..000000000
--- a/analyses/celltype-glioblastoma/notebook-template.ipynb
+++ /dev/null
@@ -1,310 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "5ecf8d71-c970-49ad-a908-fb94f43835e9",
-   "metadata": {},
-   "source": [
-    "# celltype-glioblastoma Analysis\n",
-    "\n",
-    "_Author Name_\n",
-    "\n",
-    "_Date_\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "abd58442",
-   "metadata": {},
-   "source": [
-    "## Introduction\n",
-    "\n",
-    "This a template for an analysis notebook using Jupyter.\n",
-    "\n",
-    "It is a good idea to start with a brief introduction to the analysis, including the purpose of the analysis, the data used, and the methods applied.\n",
-    "Replace this text with your own introduction, and be sure to update the _Title_, _Author Name_, and _Date_ at the top of the document.\n",
-    "\n",
-    "Don't forget to rename this file as well!\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "f7e42626",
-   "metadata": {},
-   "source": [
-    "## Setup\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "b3d030d5",
-   "metadata": {},
-   "source": [
-    "### Load modules\n",
-    "\n",
-    "Load required Python modules in the following cell.\n",
-    "We have included the standard `pathlib` module and the `session_info` module that we will be using at the bottom of this notebook to record the versions of the modules used in this analysis.\n",
-    "\n",
-    "Do not install modules here; only load them with `import` statements.\n",
-    "Avoid renaming modules with `as` statements, unless you are performing a standard renaming (e.g., `import pandas as pd`).\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "922376d5-331e-4966-910c-1f5540fdc230",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# import required modules\n",
-    "import pathlib\n",
-    "\n",
-    "import session_info"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "7f5a9354",
-   "metadata": {},
-   "source": [
-    "### Paths\n",
-    "\n",
-    "Setting paths to directories and files for input and output at the start of a notebook can be helpful for organization and reproducibility.\n",
-    "You may not know all of the paths you need when you start a notebook, but once you do, keeping them all in one place is helpful, both for yourself in the future and for other users of the notebook.\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "86d81532",
-   "metadata": {},
-   "source": [
-    "#### Base directories\n",
-    "\n",
-    "In the cell below, we include some common directories that you might need in your analysis.\n",
-    "We find the repository root by looking for a (hidden) `.git` directory somewhere in the file path that contains this file, then set the data directory and module directories relative to that.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "d124fed2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Find the repository root directory\n",
-    "repo_root = pathlib.Path.cwd()\n",
-    "while not (repo_root / \".git\").is_dir():  # search for the .git directory\n",
-    "    repo_root = repo_root.parent\n",
-    "    if repo_root == \"/\":\n",
-    "        raise FileNotFoundError(\"Could not find the repository root directory\")\n",
-    "\n",
-    "# set module path (using pathlib)\n",
-    "module_root = repo_root / \"analyses\" / \"celltype-glioblastoma\"\n",
-    "\n",
-    "# set current data directory\n",
-    "data_dir = repo_root / \"data\" / \"current\"\n",
-    "\n",
-    "# set results and plots directories (using the analysis project file to find root)\n",
-    "results_dir = module_root / \"results\"\n",
-    "plots_dir = module_root / \"plots\""
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "b40fb5e9",
-   "metadata": {},
-   "source": [
-    "#### Input and output files\n",
-    "\n",
-    "Set paths to input and output directories and files in the cell below.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "49c1e1c1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Input files\n",
-    "\n",
-    "# Output files\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "f1fbe4b6",
-   "metadata": {
-    "jp-MarkdownHeadingCollapsed": true
-   },
-   "source": [
-    "## Analysis content\n",
-    "\n",
-    "Organize the remainder of your content into sections and subsections as appropriate for your analysis.\n",
-    "\n",
-    "Add new Code and Markdown cells as needed using the Jupyter interface or your favorite keyboard shortcuts.\n",
-    "For example, you can use **Alt+Enter** on Windows or Linux or **Opt+Return** on a Mac to execute the current cell and insert a new one below.\n",
-    "\n",
-    "Be sure to comment your code and explain your steps as you go.\n",
-    "\n",
-    "It is usually a good idea to rerun the entire notebook before sharing any output, to ensure that the notebook and output files are fully up to date.\n",
-    "You can do this in the Jupyter Lab or Notebook interface by clicking on the _Kernel_ menu and choosing _Restart Kernel and Run All Cells..._\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "d1b4d0c9",
-   "metadata": {},
-   "source": [
-    "## Session Info\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "eb4d84a4",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<details>\n",
-       "<summary>Click to view session information</summary>\n",
-       "<pre>\n",
-       "-----\n",
-       "session_info        1.0.0\n",
-       "-----\n",
-       "</pre>\n",
-       "<details>\n",
-       "<summary>Click to view modules imported as dependencies</summary>\n",
-       "<pre>\n",
-       "CoreFoundation              NA\n",
-       "Foundation                  NA\n",
-       "PyObjCTools                 NA\n",
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-       "certifi                     2024.02.02\n",
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-       "comm                        0.2.2\n",
-       "cython_runtime              NA\n",
-       "dateutil                    2.8.2\n",
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-       "fqdn                        NA\n",
-       "idna                        3.6\n",
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-       "jedi                        0.19.1\n",
-       "jinja2                      3.1.3\n",
-       "json5                       0.9.24\n",
-       "jsonpointer                 2.4\n",
-       "jsonschema                  4.21.1\n",
-       "jsonschema_specifications   NA\n",
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-       "jupyter_server              2.13.0\n",
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-       "objc                        10.2\n",
-       "overrides                   NA\n",
-       "packaging                   24.0\n",
-       "parso                       0.8.3\n",
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-       "platformdirs                4.2.0\n",
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-       "pydevd_tracing              NA\n",
-       "pygments                    2.17.2\n",
-       "pythonjsonlogger            NA\n",
-       "referencing                 NA\n",
-       "requests                    2.31.0\n",
-       "rfc3339_validator           0.1.4\n",
-       "rfc3986_validator           0.1.1\n",
-       "rpds                        NA\n",
-       "ruamel                      NA\n",
-       "send2trash                  NA\n",
-       "six                         1.16.0\n",
-       "sniffio                     1.3.1\n",
-       "socks                       1.7.1\n",
-       "stack_data                  0.6.2\n",
-       "tornado                     6.4\n",
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-       "uri_template                NA\n",
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-       "websocket                   1.7.0\n",
-       "yaml                        6.0.1\n",
-       "zmq                         25.1.2\n",
-       "</pre>\n",
-       "</details> <!-- seems like this ends pre, so might as well be explicit -->\n",
-       "<pre>\n",
-       "-----\n",
-       "IPython             8.17.2\n",
-       "jupyter_client      8.6.1\n",
-       "jupyter_core        5.7.2\n",
-       "jupyterlab          4.1.5\n",
-       "notebook            7.1.2\n",
-       "-----\n",
-       "Python 3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:49:36) [Clang 16.0.6 ]\n",
-       "macOS-14.3.1-arm64-arm-64bit\n",
-       "-----\n",
-       "Session information updated at 2024-03-20 18:04\n",
-       "</pre>\n",
-       "</details>"
-      ],
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ]
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "# record the versions of the modules used in this analysis and other environment information\n",
-    "session_info.show()"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
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-    "name": "ipython",
-    "version": 3
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-   "file_extension": ".py",
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-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.8"
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- "nbformat": 4,
- "nbformat_minor": 5
-}