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BHKLab Handbook
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General
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BHKLab Handbook
bhklab/handbook
General
General
Mission Statement
Lab Space
Lab Space
Summary of Work
Summary of Work
Confluence SOW Tutorial (outdated)
Communications
Communications
BHKLab Calendar
BHKLab Gmail
Slack
Meetings
Meetings
Lab Meeting
Journal Club
Pharmacogenomics Meeting
Radiomics Meeting
Software Dev Meeting
The Meeting Owl
Presentations
Presentations
Presentations Database
Presentation Tools
Manuscripts
Manuscripts
Cover Letter
Response to Reviewers
Manuscript Review Presentations
Projects
Projects
Accomplishments Tracking
Accomplishments Tracking
Disciplines
Disciplines
Data Science
Data Science
Data Curation
Data Curation
Snakemake
ORCESTRA
IO Clinical Trial Curation
IO Clinical Trial Curation
Non-IO Clinical Trial Curation
Non-IO Clinical Trial Curation
Visualization
Visualization
Sankey Plots in R
Machine Learning
Machine Learning
Learning Resources
Tools
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
Methods
Methods
Survival Analysis
Pharmacogenomics
Pharmacogenomics
Cell Line Viability Screens
Navigating PSets
Accessing Data in a PharmacoSet
TreatmentResponseExperiment Tutorial
Imaging
Imaging
Data Sources
Data Sources
Data Types
Data Types
DICOM (Digital Imaging and Communications in Medicine)
NIfTi Format
Radiomics
Radiomics
Extraction Tools
Extraction Tools
LifeX
Radiomics Score
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
zoxide
Containerization
Containerization
Containerization on H4H
Languages
Languages
Javascript Typescript
Javascript Typescript
Learning Resources
Markdown
Markdown
Mkdocs
Mkdocs
Tabbed Code/Content Blocks
Python
Python
Rich
Rich
R
R
MultiAssayExperiment
R Coding Best Practices
SummarizedExperiment and Ranged
Tidyverse
Tidyverse
Plotting with ggplot2
networkD3
networkD3
Sankey Plot
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
UHN Onboarding Policy
BHKLab Onboarding Policy
Configuring UHN VPN
MBP Rotation Students
Lab Member Expertise
Admin Instructions
Offboarding
Offboarding
Admin Offboarding Instructions
Resources
Resources
Trainee funding opportunities
Guide for mentors and supervisors
Literature Review
Literature Review
Covidence
Paperpile
How to Read a Paper
How to Read a Paper
Contributing
Contributing
Prerequisites
Submitting Issues
Adding Content
Reviewing a Contribution
Merging Pull Requests
Conventional Commits
Release and Deployment
Handbook Changes Over Time
Projects
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