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README.txt

README.txt

CBNA: A control theory based method for identifying coding and non-coding cancer drivers

Vu VH Pham (1), Lin Liu (1), Cameron P Bracken (2,3), Gregory J Goodall (2,3), Qi Long (4), Jiuyong Li (1), and Thuc D Le (1)
(1) School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, 5095, Australia
(2) Centre for Cancer Biology, SA Pathology, Adelaide, 5000, Australia
(3) Department of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
(4) Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

This repository includes the scripts and data of the proposed method.

The scripts are in the Script folder and include:
    (1) ProposedMethod_Functions.R - Developed functions used for our method
    (2) ProposedMethod_v20.Rmd - Main script for the method
    (3) ProposedMethod_v20.html - Main script for the method in html
    (4) OtherMethods.Rmd - The script for other methods which are compared to the proposed method
    (5) OtherMethods.pdf - The script in pdf for other methods which are compared to the proposed method
    
The data are in the Data folder and include:
    (1) Input files
    (2) Output files in Output folder

Notes:
    (1) You might need to unzip hsa.zip file (TransmiR dataset for TF-miRNA interactions) before using it.
    (2) As the file BRCA_matchedData_full.RData (Tumour expression data) is larger than 100 MB, we are not allowed to upload it here, you might need to download it from https://github.com/pvvhoang/CancerDriver/releases/tag/v2.0
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