Welcome to ms-mint’s documentation!

Contents:

• Wecome to ms-mint
  • A Python library for targeted metabolomics
  • Installation
  • Documentation
  • ms-mint application with graphical user iterface (GUI)
  • Publications that used ms-mint
  • Contributions
  • Code standards
  • Usage
    • ms-mint in JupyterLab, or the Jupyter Notebook
  • Data extraction
    • Load files
    • Load target list
    • Run data extraction
    • Processing a large number of files
  • Optimize retention times
  • Plotting and data exploration
  • Plot peak shapes
  • Hierarchical clustering
  • Principal Components Analysis
  • FAQ
    • What is a target list
    • What input files can be used
    • Which properties does ms-mint extract
      • Parameters from target list
      • Results columns
  • Release Notes
    • 0.2.0 Milestones
• ms_mint
  • ms_mint package
    • Submodules
    • ms_mint.Mint module
      • Mint
    • ms_mint.chromatogram module
    • ms_mint.filelock module
      • BaseFileLock
      • FileLock
      • SoftFileLock
      • Timeout
      • UnixFileLock
      • WindowsFileLock
    • ms_mint.filters module
      • Filter
      • GaussFilter
      • Resampler
      • Smoother
    • ms_mint.io module
      • convert_ms_file_to_feather()
      • convert_ms_file_to_parquet()
      • df_to_numeric()
      • export_to_excel()
      • format_thermo_raw_file_reader_parquet()
      • ms_file_to_df()
      • mzml_to_df()
      • mzml_to_pandas_df_pyteomics()
      • mzmlb_to_df__pyteomics()
      • mzxml_to_df()
      • read_parquet()
      • set_dtypes()
    • ms_mint.matplotlib_tools module
      • hierarchical_clustering()
      • plot_metabolomics_hist2d()
      • plot_peak_shapes()
      • plot_peaks()
    • ms_mint.notebook module
      • Mint
    • ms_mint.pca module
      • PCA_Plotter
      • PrincipalComponentsAnalyser
    • ms_mint.plotly_tools module
      • get_palette_colors()
      • plotly_heatmap()
      • plotly_peak_shapes()
      • set_template()
    • ms_mint.plotting module
    • ms_mint.processing module
      • append_results()
      • extract_chromatogram_from_ms1()
      • extract_ms1_properties()
      • get_chromatogram_from_ms_file()
      • process_ms1()
      • process_ms1_file()
      • process_ms1_files_in_parallel()
      • process_ms1_from_numpy()
      • score_peaks()
      • slice_ms1_array()
    • ms_mint.standards module
    • ms_mint.targets module
      • check_targets()
      • convert_to_seconds()
      • diff_targets()
      • fill_missing_rt_values()
      • gen_target_grid()
      • read_targets()
      • standardize_targets()
    • ms_mint.tools module
      • df_diff()
      • find_peaks_in_timeseries()
      • fn_to_label()
      • formula_to_mass()
      • gaussian()
      • get_ms_files_from_results()
      • get_targets_from_results()
      • init_metadata()
      • is_ms_file()
      • lock()
      • log2p1()
      • mz_mean_width_to_min_max()
      • scale_dataframe()
    • Module contents

Indices and tables

• Index

• Module Index

• Search Page