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Natural Products Linker (NPLinker)

NPLinker is a python framework for data mining microbial natural products by integrating genomics and metabolomics data.

Original paper: Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Setup and usage

Requirement

• Linux, MacOS, or Windows with WSL (Windows Subsystem for Linux) enabled
  • For Windows without WSL, please use the docker image
• Python version ≥3.9

Installation

NPLinker is a Python package, you can install it as following:

# create a new virtual environment
python -m venv env
source env/bin/activate

# install nplinker package
pip install nplinker

# install nplinker non-pypi dependencies and databases
install-nplinker-deps

A virtual environment is required to install the the non-pypi dependencies. You can also use conda to manage python environments.

Usage

See the documentation for more information about how to use NPLinker.

Contributing

If you want to contribute to the development of nplinker, have a look at the contribution guidelines and README for developers.