/CNV

Copy Number Alteration Analysis Pipeline

Overview

This repository contains a comprehensive analysis pipeline for identifying copy number alterations in genomic data. The project utilises several key libraries, including Devtools, Biobase, QDNAseq, QDNAseq.hg38, Maftools, and Quantsmooth.

Installation

To install and set up the project, follow these steps:

  1. Clone the repository to your local machine.
  2. Install the required libraries listed in the requirements.txt file.
  3. Follow any additional installation instructions provided in the respective library documentation.

Usage

To use the analysis pipeline, follow these steps:

  1. Ensure that your processed BAM files are available in the specified format.
  2. Run each step of the analysis pipeline sequentially, as outlined in the project documentation.
  3. Refer to the README file within each library for detailed usage instructions and parameters.

Dependencies

The project relies on the following libraries:

  • Devtools
  • Biobase
  • QDNAseq
  • QDNAseq.hg38
  • Maftools
  • Quantsmooth

Ensure that these libraries are installed and properly configured in your environment before running the analysis pipeline.