https://github.com/juliuspinsker/bioconductor-learning-container
🧬 Containerized development environment for Harvard's Professional Certificate in Data Analysis for Genomics (PH525.x series). Streamlined setup for Bioconductor, R, and genomic data analysis with RStudio and DevContainer support.
https://github.com/juliuspinsker/bioconductor-learning-container
bioconductor bioinformatics chip-seq data-analysis data-science devcontainer dna-methylation docker edx functional-genomics genomics harvard harvardx ph525 ph525x r reproducible-research rna-seq rstudio single-cell-rna-seq
Last synced: about 2 months ago
JSON representation
🧬 Containerized development environment for Harvard's Professional Certificate in Data Analysis for Genomics (PH525.x series). Streamlined setup for Bioconductor, R, and genomic data analysis with RStudio and DevContainer support.
- Host: GitHub
- URL: https://github.com/juliuspinsker/bioconductor-learning-container
- Owner: JuliusPinsker
- License: mit
- Created: 2025-01-25T05:29:50.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2025-01-26T04:21:17.000Z (4 months ago)
- Last Synced: 2025-03-23T20:45:04.830Z (about 2 months ago)
- Topics: bioconductor, bioinformatics, chip-seq, data-analysis, data-science, devcontainer, dna-methylation, docker, edx, functional-genomics, genomics, harvard, harvardx, ph525, ph525x, r, reproducible-research, rna-seq, rstudio, single-cell-rna-seq
- Language: Dockerfile
- Homepage:
- Size: 9.77 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Genomics Data Analysis Learning Environment
## Overview
This repository provides a fully containerized development environment for the Professional Certificate in Data Analysis for Genomics, specifically designed to support the following Harvard Online courses:
### Courses Covered
* **PH525.5x: Introduction to Bioconductor**
* **PH525.6x: Case Studies in Functional Genomics**
* **PH525.7x: Advanced Bioconductor**
## Key Features
- 🧬 **Comprehensive Genomics Development Environment**
- 🐳 **Docker and DevContainer Support**
- 🖥️ **Browser-Accessible RStudio**
- 📚 **Pre-configured Bioconductor and R Libraries**
- 🚀 **Reproducible Research Setup**
## Prerequisites
- Docker or Podman
- Docker-compose or Podman-compose
## Quick Start
```bash
docker compose build
docker compose up -d
```
**Addendum**: You can also run these commands with Podman. In fact, Podman is recommended for its enhanced security—thanks to rootless and daemonless architecture and its more flexible licensing model.
Access RStudio at: `http://localhost:8787`
- **Username**: rstudio
- **Password**: rstudio
## Current Status
🚧 **Work in Progress**
- Currently configured for **PH525.5x: Introduction to Bioconductor**
- Libraries and setup will expand as the course progresses
## Motivation
Created to streamline the learning experience by:
- Eliminating repetitive library installation
- Providing a consistent development environment
- Reducing setup time between course sections
## Keywords
`genomics` `bioinformatics` `data-science` `r-programming` `bioconductor` `docker` `devcontainer` `RNA-seq` `ChIP-seq` `DNA-methylation` `harvard-online` `genomic-data-analysis`
## Courses Description
### PH525.5x: Introduction to Bioconductor
- Explore genome-scale data analysis
- Learn data structure and annotation
- Master normalization techniques
- Understand data interpretation strategies
### PH525.6x: Case Studies in Functional Genomics
- Practical RNA-Seq analysis
- ChIP-Seq data exploration
- DNA methylation studies
- Open-source software application
### PH525.7x: Advanced Bioconductor
- Advanced genomic visualization
- Reproducible analysis techniques
- Cloud-scale genomic data exploration
- Consortium-generated data handling
## Contributing
Contributions, suggestions, and improvements are welcome! Please open an issue or submit a pull request.
## License
This project is licensed under the [MIT License](./LICENSE).
## Acknowledgments
- Harvard Online
- Bioconductor Project
- Open-source community