Welcome to STEGO.R’s documentation!

STEGO.R is an R shiny application

Note

This project is under active development.

Contents

• Installation
  • To use STEGO, first install R, RStudio and other required programs
  • Download the project directory
  • Downloading and installing STEGO.R
  • Installing fonts
  • Running STEGO.R
  • Trouble shooting missing packages
  • Understanding the “Directory_for_Project” Folder
  • Re-installing
• Step 1. Formatting
  • Running STEGO.R
  • Manual processing
  • Automated Step 1.
• Step 2. TCRex and ClusTCR2
  • 2a. Merging TCRex
  • 2b. Clustering with ClusTCR2
  • Command line process
• Step 3. Quality control
  • 3a. Quality control of a Seurat object
  • 3b. Merging multiple Seurat objects and batch correction.
  • 3c. Annotating the Seurat object
  • 3d. Removing samples (optional)
  • 3e. Re-formatting meta-data
• Step 4. Analysis
  • Application structure
  • Uploaded files
  • Overview
  • TCR -> GEx
  • Automation (TCR -> GEX)
  • GEx -> TCR
• Post Analysis
• User Tips for the analysis
  • Tip for analysis
• Frequenctly Asked Questions
  • VDJ meta-data Questions
  • ClusTCR questions
  • Annotating
• Video Tutorial
  • Datasets
  • Quality control (Steps 1 to 3)
  • Analysis
• History
  • Version 2.0
  • Version 1.5
  • Version 1.0
• Publications and citations
  • Citing STEGO.R
  • Citing other related research