Installation

Table of contents

  1. Prerequisite
  2. Download and compile metilene3

Prerequisite

  • You can run metilene3 on Linux and macOS. If you are using Windows 10/11, WSL will be recommended.

  • If you ONLY need to call DMRs and cluster samples, you ONLY need to install:
    1. GNU Make (usually your OS has it)
    2. Python
    3. Python packages: pandas

  • If you wish to use ALL functions (e.g., annotation, visualization and GSEA), additional softwares and packages are needed:
    1. GNU Make (usually your OS has it)
    2. R and Python
    3. R packages: ChIPseeker and annotation package for TxDb object (e.g., org.Hs.eg.db, hg19, hg38, or mm10)
    4. Python packages: pandas, numpy, scikit-learn, matplotlib, seaborn, biopython, gseapy
      One simple solution to install all additional softwares and packages - use conda*:
conda create -n metilene3 -c bioconda -c conda-forge python==3.10.0 pandas scikit-learn seaborn biopython gseapy r-base bioconductor-ChIPseeker bioconductor-org.Hs.eg.db
conda activate metilene3


*GSEApy does not support python >3.11 if conda is used.

Download and compile metilene3

  • You can install metilene3 from GitHub:
git clone https://github.com/zzhu1372/metilene3.git
cd ./metilene3
make
  • Alternatively, you can also download it from Download. Extract the files and compile metilene3 under the uncompressed folder:
cd /path_to_the_downloaded_file
tar -xvzf metilene3 x.tar.gz
cd ./metilene3
make