Installation

Spectral denoising requires Python >= 3.8 installed on your system. It has been tested on Windows, Linux, and macOS platforms.

Installing from PyPI

To install the latest version of MS Entropy from PyPI, use the following command:

pip install spectral-denoising

MS Entropy package also provides many useful functions like reading .mzML/.msp/.mgf/.lbm2 files, to keep the package lightweight, these functions are not installed by default. If you need to use these functions, you can install the package with the all extra:

Dependencies

If you install Spectral denoising from PyPI, the necessary dependencies will be installed automatically. However, if you are installing from the source, install these manually:

  • chemparse==0.3.1

  • CIRpy==1.0.2

  • fuzzywuzzy==0.18.0

  • matplotlib==3.9.2

  • molmass==2021.6.18

  • ms_entropy==1.3.3

  • numexpr==2.10.1

  • numpy==2.1.1

  • pandas==2.2.3

  • plotly==5.24.1

  • PubChemPy==1.0.4

  • rdkit==2024.3.5

  • Requests==2.32.3

  • scikit_learn==1.5.2

  • scipy==1.14.1

  • seaborn==0.13.2

  • tqdm==4.66.5

Installing from Source

Spectral denoising is designed to work in python environment. Preferentially in IPython or Jupyter Notebook.

  • Downlaod and compile

    git clone https://github.com/FanzhouKong/spectral_denoising.git
cd spectral_denoising
pip install -r requirements.txt

    Then, as in Pure Python Mode, you can either copy the spectral_denoising folder to your project directory or include it in your PYTHONPATH environment variable.