uabcrmlab/crmlabbiostack repository overview

⁠crmlabBioStack

Docker images for RStudio with comprehensive R and Bioconductor package support.

⁠Current Version

Latest: v2.6.0 (2026-02-05)

⁠Quick Start

docker pull uabcrmlab/crmlabbiostack:2.6.0

docker run -d \
  -p 8787:8787 \
  -v ~/R:/data \
  -e PASSWORD=yourpassword \
  uabcrmlab/crmlabbiostack:2.6.0

Access RStudio at http://localhost:8787⁠ (user: rstudio)

⁠Included Packages (111+)

⁠Data Analysis

tidyverse, ggplot2, dplyr, tidyr, data.table, readr, purrr

⁠Bioconductor Genomics

DESeq2, edgeR, limma, biomaRt, GenomicRanges, Biostrings, SummarizedExperiment

⁠Enrichment Analysis

clusterProfiler, enrichplot, DOSE, msigdbr, gprofiler2, GOstats

⁠Visualization

ComplexHeatmap, pheatmap, ggpubr, EnhancedVolcano, PCAtools, ggsci

⁠Annotation Databases

org.Hs.eg.db, org.Mm.eg.db, GO.db, KEGGREST, reactome.db

⁠Python Integration

Streamlit, plotly, altair, numpy, pandas

⁠Usage Examples

⁠Interactive RStudio

docker run -d -p 8787:8787 -e PASSWORD=mypassword uabcrmlab/crmlabbiostack:2.6.0

⁠Run R Script

docker run --rm -v $(pwd):/workspace uabcrmlab/crmlabbiostack:2.6.0 Rscript /workspace/script.R

⁠Streamlit Web App

docker run -d -p 8501:8501 -v $(pwd):/app uabcrmlab/crmlabbiostack:2.6.0 streamlit run /app/app.py

⁠With Data Volume

docker run -d \
  -p 8787:8787 \
  -e PASSWORD=mypassword \
  -v $(pwd)/data:/home/rstudio/data \
  -v $(pwd)/projects:/home/rstudio/projects \
  uabcrmlab/crmlabbiostack:2.6.0

⁠Version History

⁠System Requirements

• RAM: 4GB minimum, 8GB recommended
• Disk: 5GB for image
• Docker: 20.10+

⁠Links

• GitHub: https://github.com/UABGH-CRMLab/crmlabBioStack⁠
• Documentation: https://github.com/UABGH-CRMLab/crmlabBioStack/tree/main/docs⁠

⁠Maintainer

C. Ryan Miller, MD, PhD University of Alabama at Birmingham [email protected]⁠

⁠License

Based on Rocker Project images. MIT License.