Overview

Protomix is a Python package designed for the preprocessing of 1H NMR metabolomics data, facilitating efficient and accurate analysis of complex metabolomic datasets. This documentation offers step-by-step tutorials and a detailed manual to guide users through the installation and usage of Protomix.

• What is Protomix?
  • Capabilities at a Glance
  • Further Information
  • Authors
    • Capabilities at a Glance
    • Further Information
    • Authors
• Installation
  • Virtual environments (recommended)
  • User installation
  • Development version
  • Experimental features
  • Virtual environments (recommended)
  • User installation
  • Development version
  • Experimental features
• Tutorial
  • Installing Protomix
  • Import packages
  • Downloading the dataset from Zenodo link
  • Unzipping the downloaded dataset
  • Extract Acquisition parameters
  • Extract Free Induction Decays (FID)
  • Remove group delay
  • Solvent residuals estimation
  • Apodization
  • Zero filling:
  • Fourier Transformation
  • Phase correction
  • Internal referencing
  • Baseline correction
  • Region removal
  • Negative values zeroing
  • Icoshift class
  • Peak alignment dataframe
  • Window selection
  • Binning
  • Normalization
  • Installing Protomix
  • Import packages
  • Downloading the dataset from Zenodo link
  • Unzipping the downloaded dataset
  • Extract Acquisition parameters
  • Extract Free Induction Decays (FID)
  • Remove group delay
  • Solvent residuals estimation
  • Apodization
  • Zero filling:
  • Fourier Transformation
  • Phase correction
  • Internal referencing
  • Baseline correction
  • Region removal
  • Negative values zeroing
  • Icoshift class
  • Peak alignment dataframe
  • Window selection
  • Binning
  • Normalization
• Module Documentation
  • Protomix.extract_fids
    • extract_fids()
  • Protomix.extract_params
  • Protomix.group_delay_removal
  • Protomix.solvent_residuals_removal
  • Protomix.apodization
  • Protomix.zero_filling
  • Protomix.fourier_transform
  • Protomix.internal_referencing
  • Protomix.phase_correction
  • Protomix.baseline_correction
  • Protomix.Icoshift class
  • Protomix.negative_values_zeroing
  • Protomix.window_selection
  • Protomix.region_removal
  • Protomix.binning
  • Protomix.normalize
  • Protomix.extract_fids
    • extract_fids()
  • Protomix.extract_params
    • extract_params()
  • Protomix.group_delay_removal
    • group_delay_removal()
  • Protomix.solvent_residuals_removal
    • solvent_residuals_removal()
  • Protomix.apodization
    • apodization()
  • Protomix.zero_filling
    • zero_filling()
  • Protomix.fourier_transform
    • fourier_transform()
  • Protomix.internal_referencing
    • internal_referencing()
  • Protomix.phase_correction
    • phase_correction()
  • Protomix.baseline_correction
    • baseline_correction()
  • Protomix.Icoshift class
    • Icoshift
      • Icoshift.run()
  • Protomix.negative_values_zeroing
    • negative_values_zeroing()
  • Protomix.window_selection
    • window_selection()
  • Protomix.region_removal
    • region_removal()
  • Protomix.binning
    • binning()
  • Protomix.normalize
    • normalize()