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General
Disciplines
Software Development
Grants
Onboarding / Offboarding
Resources
Contributing

BHKLab Handbook

bhklab/handbook

General
General
- Mission Statement
- Lab Space
  Lab Space
- Summary of Work
  Summary of Work
  - Confluence SOW Tutorial (outdated)
- Communications
  Communications
- Meetings
  Meetings
- Presentations
  Presentations
  - Presentations Database
  - Presentation Tools
- Manuscripts
  Manuscripts
- Projects
  Projects
- Accomplishments Tracking
  Accomplishments Tracking
Disciplines
Disciplines
- Data Science
  Data Science
  - Data Curation
    
    Data Curation
    
    Clinical Trial Curation
    
    Clinical Trial Curation
- Machine Learning
  Machine Learning
  - Learning Resources
  - Tools Tools
    Table of contents
    
    Python Libraries
    
    Deep Learning & Accelerator-Enabled Computing
    
    R Libraries
  - Supervised Learning
    
    Supervised Learning
  - Unsupervised Learning
    
    Unsupervised Learning
    
    Clustering
    
    Clustering
    
    GMM
    
    K-Means Clustering
    
    Spectral Clustering
    
    Dimensionality Reduction
    
    Dimensionality Reduction
    
    Laplacian Eigenmaps
    
    Locally Linear Embeddings
    
    Principal Component Analysis (PCA)
    
    Random Projections
    
    T-SNE
    
    UMAP
    
    Generative Modeling
    
    Generative Modeling
    
    VAE
- Bioinformatics
  Bioinformatics
  - Data Types
    Data Types
    
    RNA-Seq
  - Tools
    Tools
    
    RNA-Seq Pipelines
    RNA-Seq Pipelines
    
    DESeq2
    
    Kallisto
    
    STAR
- Pharmacogenomics
  Pharmacogenomics
  - Cell Line Viability Screens
  - Navigating PSets
- Imaging
  Imaging
  - Data Sources
    
    Data Sources
  - 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
    
    Windows Subsystem for Linux (WSL)
  - Integrated Development Environments (IDEs)
    
    Integrated Development Environments (IDEs)
    
    RStudio
    
    Visual Studio Code
  - Package Managers
    
    Package Managers
    
    Pixi Package Manager
  - CLI Tools
    
    CLI Tools
  - Containerization
    
    Containerization
- Languages
  Languages
  - Javascript Typescript
    
    Javascript Typescript
    
    Learning Resources
  - Markdown
    
    Markdown
    
    Mkdocs
    
    Mkdocs
    
    Tabbed Code/Content Blocks
  - Python
    
    Python
  - R
    
    R
    
    MultiAssayExperiment
    
    Tidyverse
    
    Tidyverse
    
    Plotting with ggplot2
  - Rust
    
    Rust
  - SQL
    
    SQL
- 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
  - ORCESTRA Version Controlling
- Remote Development
  Remote Development
  - Google Cloud Platform
    Google Cloud Platform
    
    Introduction to Google Cloud Platform (GCP)
    
    Google Cloud Vertex AI
    
    Google Cloud Artifact Registry
    
    BigQuery
    
    Cloud SQL for MySQL, PostgreSQL, and Microsoft SQL Server
    
    Compute Engine
    
    Google Cloud Storage (GCS)
    
    Serving Images and Videos From A Bucket
    
    GCP Virtual Machines (VMs)
  - High Performance Computing for Health
    
    High Performance Computing for Health
    
    Quick Start
  - Lab Server
    
    Lab Server
    
    GitHub Access
  - Compute Canada Cloud
    
    Compute Canada Cloud
Grants
Grants
- Identifying Suitable Grants
- Preparing for Submission
  Preparing for Submission
  - UHN Budget Process
- Writing a Strong Grant Proposal
- Submission Process
- Templates & Resources
Onboarding / Offboarding
Onboarding / Offboarding
- Onboarding
  Onboarding
- Offboarding
  Offboarding
  - Admin Offboarding Instructions
Resources
Resources
- Trainee funding opportunities
- Guide for mentors and supervisors
Contributing
Contributing

Table of contents

Python Libraries
- Deep Learning & Accelerator-Enabled Computing
R Libraries

Tools#

Python Libraries#

Deep Learning & Accelerator-Enabled Computing#

PyTorch
Lightning

R Libraries#

glmnet

June 26, 2025 April 30, 2025

James Bannon, Katy Scott

Learning Resources