KRSA Report and Kinome Analysis Template

Overview

This repository provides a standardized, reproducible workflow for Kinome Analysis using tools from the Cognitive Disorders Research Lab.

Features

• Generate comprehensive KRSA reports for kinome array experiments
• Perform Universal Kinase Analysis (UKA)
• Create Creedenzymatic results
• Generate detailed quartile plots
• Standardize data and results management
• Ensure reproducible research workflows

Requirements

Software Prerequisites

1. R (Statistical Computing)

   • Download from R Project Website
   • Recommended: Latest stable version

2. Git (Version Control)

   • Download from Git Website
   • Ensures proper version tracking

3. Just (Task Runner)

   • Install via: The installation documentation Just Documentation
   • Manages project workflows

4. Quarto (Rendering Engine)

   • Install via: The installers on the Quarto Website
   • Handles the conversion of R Markdown files to Markdown with the R code evaluated.

5. Text Editor/IDE Recommended options:

   • Visual Studio Code
   • RStudio
   • Neovim

6. Additional Requirements

   • Windows Only: Rtools
   • Optional: Radian (Enhanced R Console)

Quickstart Guide

1. Repository Setup

1. Click "Use Template" to create a new repository

2. Clone the repository to your local machine

   git clone <your-repository-url>
   cd <repository-name>

2. Environment Preparation

1. Open R in the repository directory

2. Restore project dependencies

   renv::restore()

3. Data Preparation

1. Place SigmBg and SignalSaturation files in the kinome_data/ directory

2. Create a new analysis file from the template

   just new-analysis my_experiment

4. Configuration

1. Edit the newly created .Rmd file
2. Update file paths in the YAML frontmatter
3. Set chip type and prefix as needed

5. Run Analysis

Execute the complete workflow:

just render
just all

Available Just Commands

Command	Description
just list	Show all available commands
just new-analysis NAME	Create a new analysis from template
just render	Render all Markdown reports
just uka	Run Universal Kinase Analysis
just creeden	Run Creedenzymatic analysis and generate quartile plots
just clean	Remove generated files and artifacts

Troubleshooting

• Ensure all dependencies are installed
• Check R and Just versions
• Verify data file locations

License

Everything in this project is licensed under the MIT license except for the UKA_* files in the reference_data folder.

Contact

In case of any problems, please file an issue