Installation

Download

dds_analysis is written in Python. It can be installed and accessed from the command line and is available for both Linux and macOS operating systems. The package can be downloaded here. Alternatively, you can use the following command:

$ wget https://github.com/dmr-analysis/dds-analysis/archive/refs/heads/master.zip

Please send email to Dr. Junbai Wang (junbai.wang@medisin.uio.no) for requesting a free download of full DDS-analysis pacakge.

Please include your name, Institution/company name, Email of your institute or company (do not use gmail or yahoo email etc), and a brief description of the purpose for using bpb3 package.

Please use the subject title “bpb3/dds/dmr request “ for your email.

Install

It is highly recommended to create a separate virtual environment for the package to avoid any library conflicts. You can create a virtual environment using the following commands. We recommend installing and using Miniconda/Anaconda (Miniconda). You can find a tutorial on creating and updating virtual environments here.

If Miniconda is already installed, you can proceed with the following step-by-step installation. We have provided a quick installation setup file named quick_install.sh for your convenience. Running a simple bash command will automatically prepare the package for use:

$ ./quick_install

If the quick_install.sh script is unsuccessful, you can follow the step-by-step details provided below:

  1. Create a virtual environment:

$ conda create --name dmr_env python==3.9.16

  1. Activate the virtual environment:

$ conda activate dmr_env

  1. Install pip if not already installed:

$ conda install pip

Please allow any other installations when prompted.

Requirements

Before installing the package, the dependencies must be fulfilled. It is advised to install the dependencies using Miniconda. The list of dependencies is as follows:

  • matplotlib==3.5.3

  • numpy==1.21.5

  • pandas==1.4.4

  • scikit_learn==1.2.2

  • scipy==1.9.1

  • setuptools==65.6.3

  • statsmodels==0.13.5

  • bedtools==2.27.0

These dependencies can be installed one by one using the Conda package manager. For example:

$ conda install numpy==1.21.5

A requirements.txt file is provided with the package. You can automatically install all the requirements using the following command:

$ conda install --file requirements.txt

Alternatively, you can install the requirements using pip:

$ pip install -r requirements.txt

Package Installation

To install the package, navigate to the dds_analysis directory (the folder containing setup.py and pyproject.toml) and run the following command:

$ pip install .

For more details, refer to the readme file in the package.

Package Contents

The package folder will contain the following:

  • demo: Contains function scripts.

  • dds_analysis: Contains the Python source code of the pipeline.

  • readme.txt: Instructions about the usage of the package.

  • requirements.txt: List of requirements that can be used for automatic installation using Miniconda or pip.

  • setup.py: Setup file for the package.

  • project.toml: Setup file for the package.

  • data: Contains input and output data for the secondary functions.