Installation

Table of contents

1. Prerequisite
2. Download and compile metilene3

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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 (tested on python==3.10.0)
  3. Python packages: pandas (tested on pandas==1.5.1)
     
     
• If you wish to use ALL functions (e.g., annotation, visualization and GSEA), additional software 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, pandarallel
     One simple solution to install all additional software and packages - use conda:

conda create -y -n metilene3 -c bioconda -c conda-forge python==3.10.0 pandas pandarallel scikit-learn seaborn biopython gseapy r-base bioconductor-ChIPseeker bioconductor-org.Hs.eg.db bioconductor-txdb.hsapiens.ucsc.hg19.knowngene bioconductor-txdb.hsapiens.ucsc.hg38.knowngene
conda activate metilene3

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 metilene3-3.1.tar.gz
cd ./metilene3-3.1
make