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BHKLab Handbook

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bhklab/handbook

BHKLab Handbook

bhklab/handbook

General
General
- Mission Statement
- Code Of Conduct
  Code Of Conduct
- Summary of Work
  Summary of Work
  - Confluence SOW Tutorial (outdated)
- Communications
  Communications
  - BHKLab Calendar
  - BHKLab Gmail
- Meetings
  Meetings
- Presentations
  Presentations
  - Presentations Database
  - Presentation Tools
- Manuscripts
  Manuscripts
- Projects
  Projects
Disciplines
Disciplines
- Data Science
  Data Science
  - Data Curation
    
    Data Curation
    
    Clinical Trial Curation
    
    Clinical Trial Curation
- Machine Learning
  Machine Learning
- Bioinformatics
  Bioinformatics
  - Data Types
    Data Types
    
    RNA-Seq
  - STAR Alignment Guide
  - DESeq2
- Pharmacogenomics
  Pharmacogenomics
- Imaging
  Imaging
  - Data Types
    Data Types
    
    DICOM (Digital Imaging and Communications in Medicine)
    
    NIfTi Format
  - Radiomics
    
    Radiomics
  - Tools
    
    Tools
    
    QIPCM
    
    QIPCM
    
    Querying Data from the QIPCM PACS
Software Development
Software Development
- Development Environment
  Development Environment
  - Shells
    
    Shells
  - Integrated Development Environments (IDEs)
    
    Integrated Development Environments (IDEs)
  - Package Managers
    
    Package Managers
  - CLI Tools
    
    CLI Tools
  - Containerization
    
    Containerization
- Languages
  Languages
  - Javascript Typescript
    
    Javascript Typescript
  - Markdown
    
    Markdown
    
    Mkdocs
    
    Mkdocs
    
    Tabbed Code/Content Blocks
  - Python
    
    Python
  - R
    
    R
    
    Tidyverse
    
    Tidyverse
    
    Plotting with ggplot2
  - Rust
    
    Rust
- Version Control
  Version Control
  - Git
    Git
    
    Introduction
    
    Quick Git Tips
  - Code Reviews
    Code Reviews
    
    Introduction to Code Reviews
    
    Mindsets in Code Reviews
    
    Common Challenges and Solutions in Code Reviews
    
    Conducting a Review
    
    Code Review Presentation
- Remote Development
  Remote Development
  - Google Cloud Platform
    Google Cloud Platform
    
    Introduction to Google Cloud Platform (GCP)
    
    Google Cloud Artifact Registry
    
    BigQuery
    
    Cloud SQL for MySQL, PostgreSQL, and Microsoft SQL Server
    
    Google Cloud Storage (GCS)
    
    GCP Virtual Machines (VMs)
  - High Performance Computing for Health
    
    High Performance Computing for Health
  - Lab Server
    
    Lab Server
    
    GitHub Access
  - Compute Canada Cloud
    
    Compute Canada Cloud
Onboarding / Offboarding
Onboarding / Offboarding
- Onboarding
  Onboarding
- Offboarding
  Offboarding
Resources
Resources
- Trainee funding opportunities
Contributing
Contributing

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