This repository provides comprehensive, hands-on workshop materials for bioinformatics data analysis, targeting biologists with beginner to intermediate R and/or bash skills. The modules enable participants to perform various analyses, offering a structured learning path for computational biology topics.

How It Works

The materials are structured as short, half-day workshops, typically 2-3 hours long. They guide participants through practical data analysis tasks using R/RStudio and Shell/bash environments. The repository organizes lessons by topic, clearly outlining prerequisites and providing links to detailed instructions and resources for each workshop.

Quick Start & Requirements

• Install/Run: No specific installation command is provided; materials are designed for workshop environments. Users will need R/RStudio and a shell environment (e.g., bash).
• Prerequisites: Varies by workshop, ranging from no prerequisites to foundational R or Shell knowledge. Specific software like Git, GitHub, and potentially bioinformatics tools (e.g., GEMINI) may be required for advanced topics.
• Resources: Links to workshop introduction slides and detailed preparation instructions are available within the repository.

Highlighted Details

• Covers a wide range of bioinformatics topics, from R and Shell fundamentals to advanced analyses like differential gene expression, data visualization, and RNA-seq.
• Includes workshops on essential computational skills such as Git/GitHub for version control and reproducible reporting with RMarkdown.
• Features specialized workshops like "Interactive Data Visualization with Shiny in R" and "Introduction to scRNA-seq."
• Materials are developed by the Harvard Chan Bioinformatics Core (HBC).

Maintenance & Community

• Developed by the teaching team at the Harvard Chan Bioinformatics Core (HBC).
• No specific community links (Discord/Slack) or roadmap are provided in the README.

Licensing & Compatibility

• License: Creative Commons Attribution 4.0 International (CC BY 4.0).
• Restrictions: Permits unrestricted use, distribution, and reproduction, provided original author and source are credited. Suitable for commercial use and integration into closed-source projects, with attribution.

Limitations & Caveats

The repository focuses on providing workshop materials rather than a runnable software package. Users must independently set up the required software environments and dependencies for each workshop. Some workshop registration links are marked as "Closed."