TRC Scripts (RNA-miRNA-circRNA Interaction Scoring)

This repository contains a collection of R scripts and tools for scoring and analyzing interactions between various RNA species (mRNA, miRNA, and circRNA), with a focus on calculating absolute Total RNA Concentration (TRC) and MITscores.

Project Structure

• scripts/: Primary analysis scripts.
  • core/: Latest stable versions of the scoring and TRC calculation logic.
  • correction/: Scripts for NGS data correction (e.g., voom).
  • experimental/: Latest iterations, including seed proportion and TrT ratio calculations.
  • utility/: General helper functions.
• tests/: Data validation and consistency checks.
• plots/: Diagnostic and exploratory plots (density, mean-variance, QQ-plots).
• docs/: Documentation and protocols.
• archive/: Older versions of scripts for reference.

Getting Started

Prerequisites

Common R packages required:

• limma
• dplyr
• edgeR
• ggplot2

See the DESCRIPTION file for a full list of dependencies.

Configuration

Most scripts require setting base directory paths. Look for these variables at the start of each script:

• basedir: Root directory for analysis.
• RNAdir: Path to mRNA quantification data (e.g., Salmon).
• miRNAdir: Path to miRNA quantification data (e.g., miRge2).
• INTERdir: Path to interaction table files.
• OUTPUTdir: Target directory for results.

Citation

If you use these scripts in your research, please cite them using the information in CITATION.cff.

License

This project is licensed under the MIT License - see the LICENSE file for details.