Satish, AL; Kumar P; Morbia I and Singh, U (2026).

Meta analysis of FANTOM CAGE and GENCODE data to describe properties of transcription start site alteration in cancers.

This repository contains all the custom scripts written to process the data as shown in the manuscript. The scripts are written in bash or R (version 4.4.1). The scripts are organized to facilitate full reproduction of the statistical analysis and figures presented in the paper. All the input data that need to be invoked are available as supplementary tables in the manuscript.

Repository Structure

The repository is organized as follows:

• scripts/: Contains all source code in R and Shell for the analysis.

  • 01_data_processing/: Scripts for data downloading and pre-processing.

  • 02_main_analysis/: Scripts for deriving parameters and performing statistical analysis.

  • 03_figures_tables/: Scripts for generating all manuscript figures and tables.

• data/: Contains the raw and processed data necessary to run the scripts.

  • 01_raw_genome/: Downloaded raw genomic data.

  • 02_processed_genome/: Genome data post-processing.

  • 03_analysis_repository/: Derived parameters from processed genome data.

Note: All public data sources are referenced below. Tables generated are available in the supplementary table of the manuscript for cross-referencing.

• results/: Contains generated figures, tables, and other outputs.

Prerequisites

This project requires R (version 4.4) or above and the following R packages:

1. Mandatory packages for data import, manipulation and export

• tidyverse (version 2.0.0)
• magrittr (version 2.0.3)

2. Packages for data visualisation\

• scales (version 1.3.0)
• ggExtra (version 0.10.1)
• patchwork (version 1.3.0)

3. Packages for advanced statistics and analyses\

• psych (version 2.4.6.26)
• cocor (version 1.1)
• collapse (version 2.0.19)
• PCAtools (version 2.16.0)
• car (version 3.1)

4. Packages from bioconductor for 5'UTR benchmarking

• "plyranges" (version 1.24.0)
• rtracklayer (version 1.64.0)
• BiocGenerics (version 0.50.0)

All required R packages can be installed by running the script scripts/install_packages.R.

Installation and Setup

1. Clone the repository: (bash)

   git clone https://github.com/Aditi-Satish/Manuscript-1.git

   cd``Manuscript-1

2. Install dependencies: Open R and run the dependent R packages as mentioned above.

3. Download data: Data was sourced from UCSC, Riken Institute and GENCODE. Follow the steps in the 'download_raw_data' file and place them in the data/01_raw_genome/ folder.

Processing the raw genome data

Follow the steps in the scripts/01_data_processing/ to process the downloaded genomic data. This includes TSS annotation and curation of CAGE data.

References

• Manuscript: Manuscript is available on at [Link to Pre-print].

Acknowledgments

This research was supported by a grant from PMRF.