CnSubclonalityProject

Intra-tumoral heterogeneity (ITH) of somatic copy number alterations (ITH-SCNAs) in diffuse glioma.

Overview

Purpose of this repository is to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in.

Repo Contents

• code: tidy R functions and R script.
• data: original and preprocessed data used for analysis and share.
• result: important middle results and final results of manuscript, most of them are in form of .RData, which can be easily loaded and operated by R.

Instructions for Use

For readers who want to obtain raw/result data, locate data file, then download it with one of following ways:

• In Github, download file by clicking either Download button or Raw button at corresponding data page

• Use linux command wget or curl, fo example, you can download PCNA gene sets by

  wget https://github.com/BioinfoDriver/CnSubclonalityProject/tree/main/data/PCNA_Signature.txt

Or you can download whole respository with one of following ways:

• Clone this repository with git clone https://github.com/BioinfoDriver/CnSubclonalityProject.git

• Download whole respository by clicking Download button at top right of url page https://github.com/BioinfoDriver/CnSubclonalityProject

Reproduce analysis

For readers who want to reproduce analysis shown in manuscript, please install R in your computer.

Test Environment

• System: Linux
• Software: R v4.0.2