KRSA Report and Kinome Analysis Template

This repository includes a series of scripts and other files that make it easier and quicker to generate Kinome Analysis using the Cognitive Disorders Research Lab set of tools.

Features

This template allows you to perform the following tasks:

• Generate KRSA reports for a given kinome array experiment dataset
• Generate UKA results for a given kinome array experiment dataset
• Generate creedenzymatic results for the experiments
• Generate Quartile plots for the experiments

In addition, this repository allows for the following:

• Standardizing the location of particular input and output files
• Allow for easy and predictable management of the data and results
• Allow for easy publishing of the results in a reproducible manner

Requirements

Use of this repository requires the following tools to already be installed:

1. R -- The language runtime
2. git -- A version control system
3. just -- A task runner
4. A text editor or IDE ( Visual Studio Code, RStudio, Neovim etc.)
5. (For Windows Only) Rtools for your version of R.
6. (Optional) radian -- An alternative R Console

Quickstart

Follow this process for a quick start:

1. Use the [Use Template] button to generate a copy of the repository in your own account.
2. Clone this repository to your own computer.
3. Open R in the repository directory.
4. Run renv::restore() in the R Console and install all the dependencies.
5. Place your SigmBg and SignalSaturation files in the kinome_data folder.
6. Copy the template.Rmd file to your report name.
7. Change the file paths in the top matter of the Rmd file to point to the files you just placed.
8. Run just all in the console.