JupyterLab R Environment

A Reproducible Docker Environment for Statistical Analysis in R

A Docker-based JupyterLab environment with R as the kernel, designed for reproducible data analysis. All R and Python package versions are pinned via renv.lock and requirements.txt so that the analysis environment can be reconstructed exactly on any machine.

Table of Contents

1. Getting Started
   • Prerequisites
   • Installation
2. HTTPS Support
3. Package Management
4. Pre-installed R Packages
5. Pre-installed Bioconductor Packages
6. Versioning
7. License

Getting Started

Prerequisites

• Docker Desktop
• Git
• mkcert — optional, for HTTPS support (see HTTPS Support)

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Installation

1. Clone the Repository

git clone git@github.com:SamThilmany/JupyterLab-with-R--Docker-Environment.git
cd JupyterLab-with-R--Docker-Environment

2. Build the Docker Image

cd jupyter-r
docker compose build

The image is pinned to linux/amd64 because rawrr's .NET assembly is only available as an x86-64 binary on Linux. On Apple Silicon (M1/M2/M3/…), Docker Desktop runs the container via Rosetta 2 — no additional configuration is required.

Building downloads all R and Python packages and may take several minutes depending on network speed. If the build fails due to a transient download error, re-running the command is safe — Docker caches completed layers and renv retries failed package downloads automatically.

3. Start the Container

docker compose up -d

The container restarts automatically after Docker Desktop or system restarts.

4. Access JupyterLab

Open a browser and navigate to:

• https://localhost:8888 — if HTTPS certificates are configured (see below)
• http://localhost:8888 — fallback when no certificates are present

5. Stop the Container

docker compose down

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HTTPS Support

JupyterLab can be served over HTTPS using a locally-trusted certificate generated by mkcert. This avoids browser security warnings without requiring any exceptions to be added manually.

macOS

brew install mkcert
mkcert -install

mkdir -p jupyter-r/certs
cd jupyter-r/certs
mkcert localhost 127.0.0.1
mv localhost+1.pem cert.pem
mv localhost+1-key.pem key.pem

Windows

choco install mkcert
mkcert -install

mkdir jupyter-r\certs
cd jupyter-r\certs
mkcert localhost 127.0.0.1
Rename-Item localhost+1.pem cert.pem
Rename-Item localhost+1-key.pem key.pem

After placing the certificate files, restart the container:

docker compose restart jupyter

The server falls back to HTTP automatically when no certificate files are present, so the setup remains functional on machines without mkcert configured.

Note: The jupyter-r/certs/ directory is excluded from version control. Do not commit certificate files.

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Package Management

R packages are installed from renv.lock, which records the exact version of every package in the image. Python packages are pinned in requirements.txt. Both files are committed to the repository to ensure that any rebuild produces an identical environment.

Adding R Packages

1. Add the package name to the appropriate list in jupyter-r/install_packages.R.
2. Delete jupyter-r/renv.lock to force a fresh install.
3. Rebuild the image:

   docker compose build

4. On the next docker compose up, the updated renv.lock is copied to the notebooks/ directory. Move it to jupyter-r/ and commit it:

   mv notebooks/renv.lock jupyter-r/renv.lock
   git add jupyter-r/renv.lock
   git commit -m "add <package-name>"

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Pre-installed R Packages

Package	Description
IRkernel, IRdisplay, repr	R kernel for JupyterLab
languageserver	R language server for editor support
devtools	Package development tools
tidyverse	Collection of data science packages (dplyr, ggplot2, tidyr, …)
ggplot2	Grammar of graphics plotting
ggfortify	ggplot2 extensions for statistical objects
ggforce	ggplot2 extension with additional geoms
ggtext	Markdown and HTML text rendering in ggplot2
ggrepel	Non-overlapping text labels for ggplot2
GGally	ggplot2 extension for matrix plots and model diagnostics
ggVennDiagram	Venn diagram geoms for ggplot2
eulerr	Euler and Venn diagrams
patchwork	Composing multiple ggplot2 panels
cowplot	Plot arrangement and annotation
metR	Meteorological and geophysical field visualisation
scales	Scale functions for visualisation
showtext	Custom font rendering in R graphics
RColorBrewer	Colour palettes for data visualisation
doParallel	Parallel computing backend
combinat	Combinatorics utilities
s2	Spherical geometry

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Pre-installed Bioconductor Packages

Package	Description
rawrr	Direct access to Thermo raw mass spectrometry data
limma	Linear models for microarray and RNA-seq data
fgsea	Fast gene set enrichment analysis
clusterProfiler	Statistical analysis of functional gene clusters
enrichplot	Visualisation of functional enrichment results
DOSE	Disease ontology semantic and enrichment analysis
biomaRt	Interface to BioMart databases (Ensembl, etc.)
AnnotationDbi	Annotation database interface
org.Hs.eg.db	Human genome-wide annotation
ComplexHeatmap	Complex heatmap and annotation visualisation
circlize	Circular visualisation
MSstats	Statistical analysis of quantitative mass spectrometry data
MSstatsTMT	MSstats extension for TMT labelling experiments

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Versioning

Semantic Versioning is used for versioning. For available versions, see the Releases.

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License

This project is distributed under the Apache License 2.0. See LICENSE for more information.

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