/MiRNA-for-Cancer

Primary LanguagePython

MiRNA-for-Cancer

InForMir Code Documentation

Introduction:

Welcome to the documentation for InForMir codes. This document will guide you through the steps necessary to set up and execute the codes successfully.

Prerequisites:

Before running the codes, ensure that the following prerequisites are met:

  1. Python
  2. Microsoft Excel Installation:
  3. Clone the repository from https://github.com/MariaSmrity/MiRNA-for-Cancer.git to your local machine.
  4. Navigate to the project directory.
  5. Install the required dependencies using the following command: [Your package manager] install [dependencies]

Running the Codes: Follow these steps to execute the codes:

  1. Open your terminal/command prompt.

  2. Navigate to the project directory.

  3. Have “mir-gene-interaction.csv” in the drive. a. Run “seperate_chromosome__from_mainFile.py” // where main file is mir-gene-interaction.csv, output file is “Target.csv” b. Run “CoopOrCom.py” // it will create Final.CSV c. Run “SeperateFileForCancerType.py” // it will separate Final.csv into cancertype.csv files d.Run “Mir1_2 Scores Compare.py” // it will plot and save mir1 and mir2 scores.

  4. Have “InFormiR_TCGA-data-download-link 1.csv” in your drive. a. Run “download_files.py” //It will download files for sample patients b. Run “unzip files.py” to unzip downloaded files to the desired location c.Run “Create Correlation file.py” //generate file with desired format from downloaded files d. Run “calculate_correlation.py” // Update file with correlation values e. Finally Run “plot_correlation.py” // plot and save files in folder